Samaranch was admitted to the Quiron Hospital in Barcelona on Sunday after experiencing heart trouble. The hospital said he died at 1:25 p.m.
"If there is a good way to die, I guess it was this way," Juan Antonio Samaranch Jr. told The Associated Press. "He had a full life and career."
IOC president Jacques Rogge will be among the dignitaries attending a special ceremony on Thursday morning before the funeral at Barcelona's cathedral later that day.
"I cannot find the words to express the distress of the Olympic family," Rogge said in a statement. "I am personally deeply saddened by the death of the man who built up the Olympic Games of the modern era, a man who inspired me, and whose knowledge of sport was truly exceptional."
Small in stature and shy by nature, Samaranch appeared uncomfortable appearing or speaking in public. But behind the scenes, he was a skilled and sometimes ruthless operator who could forge consensus in the often fractious Olympic movement and push IOC members to deliver exactly what he wanted.
Samaranch was also a lightning rod for critics, who attacked him for his ties to the Franco era in Spain, his autocratic style and the IOC's involvement in the Salt Lake City corruption scandal.
The Samaranch era was perhaps the most eventful in IOC history, spanning political boycotts, the end of amateurism and the advent of professionalism, the explosion of commercialization, a boom in growth and popularity of the games, the scourge of doping, and the Salt Lake crisis.
Samaranch had been bothered by health problems ever since stepping down nine years ago. He was hospitalized for 11 days in Switzerland with "extreme fatigue" in 2001 after returning from the IOC session in Moscow, where Rogge was elected as his successor.
Samaranch was hospitalized shortly afterward in Barcelona for what was described as high blood pressure. He received regular dialysis treatment for kidney trouble. He spent two days in a hospital in Madrid in 2007 after a dizzy spell, and underwent hospital checks in Monaco in October 2009 after feeling ill at a sports conference.
Despite the advancing age and medical troubles, Samaranch continued to travel to IOC meetings around the world. He looked increasingly frail in recent months. Attending the IOC session at the Winter Games in Vancouver in February, he walked with the aid of a female assistant.
Even in retirement, Samaranch remained active in Olympic circles and tried to help Madrid secure the games of 2012 and 2016. Madrid finished third behind winner London and Paris in the 2005 vote for the 2012 Olympics, and second to Rio de Janeiro for 2016.
Samaranch spoke during Madrid's presentation in Copenhagen on Oct. 2, 2009, essentially asking IOC members to send the games to the Spanish capital as a parting gift for an old man close to his final days.
"Dear colleagues, I know that I am very near the end of my time," Samaranch said. "I am, as you know, 89 years old. May I ask you to consider granting my country the honor and also the duty to organize the games and Paralympics in 2016."
In Moscow in 1980, as a little-known Spanish diplomat, Samaranch was elected the seventh president of the IOC, taking the most powerful job in global sports.
Twenty-one years later, as a well-known world figure, Samaranch returned to Moscow to finish his term -- basking in the unprecedented popularity and riches of the games but still bearing the scars of the scandal that led to the ouster of 10 IOC members for receiving improper benefits from the 2002 Salt Lake bid committee.
While his closest friends said Samaranch was extremely emotional and sentimental, outwardly he remained cool and philosophical in his final days in office.
"I'm feeling OK," he said. "Life is life. There is a beginning and an end. This is the end of my presidency. I've known for a long time that this day was coming."
Even at the end of his Olympic reign in 2001, Samaranch worked hard to achieve three electoral victories as part of his final legacy: the awarding of the 2008 Olympics to Beijing, the election of Rogge as the new president, and the appointment of his son, Juan Antonio Jr., as an IOC member.
Samaranch retired as the second-longest serving president in the history of the IOC. Only Pierre de Coubertin, the French baron who founded the modern Olympics, was in office longer, serving for 29 years (1896-1925). American Avery Brundage served for 20 years (1952-72).
Samaranch was the last IOC leader to stay in office for so long. Under new rules, the maximum term for the president is 12 years (one eight-year mandate, plus the possibility of an additional four-year term). Rogge was re-elected unopposed to a second term in Copenhagen on Oct. 9, 2009, extending his period in office until 2013.
"After de Coubertin, there is no question that Samaranch stands head and shoulders above the other presidents in terms of his impact, not only on the Olympic Games but the place of the Olympic movement in the world," Olympic historian John MacAloon said.
Longtime Canadian IOC member Dick Pound, who finished third in the voting to Rogge, said Samaranch was one of three "great or defining presidents."
"De Coubertin to get it going, Brundage to hold it together through a very difficult period, and Samaranch to bring it from the kitchen table to the world stage," Pound said.
Samaranch spoke of the dramatic changes himself.
"You have to compare what is the Olympics today with what was the Olympics 20 years ago -- that is my legacy," he said before his retirement. "It is much more important. Also, all our sources of finances are coming from private sources, not a single dollar from the government. That means we can assure our independence and autonomy.
"And the most important thing -- it is easy to say but not to get -- is the unity with the national Olympic committees and mainly with the international federations."
When Samaranch came to power in 1980, the IOC was virtually bankrupt and the Olympics were battered by boycotts, terrorism and financial troubles.
When he left, the IOC's coffers were bulging from billions of dollars in commercial revenues, the boycott era was over, and the games were firmly established as the world's favorite sports festival.
"He took a very badly fragmented, disorganized and impecunious organization and built it into a universal, united and financially and politically independent organization that has credibility, not only in the world of sport, but also in political circles," Pound said. "That's an enormous achievement to accomplish in 20 years."
Samaranch's presidency was also clouded by controversy. He was hounded by critics who said the games were over-commercialized and riddled with performance-enhancing drugs, and that he perpetuated the IOC image of a private club for a pampered elite.
British author Andrew Jennings, one of Samaranch's most virulent critics, wrote that "corruption became the lubrication of his Olympic industry" and that he "fleeced sport of its moral and monetary value."
Samaranch's reputation was scarred most of all by the Salt Lake City scandal, which led to the expulsion of six IOC members and resignation of four others who benefited from more than $1 million in cash, gifts, scholarships and other favors doled out during the Utah capital's winning bid for the 2002 Winter Games.
"What I regret, really regret, is what happened in Salt Lake City," he said.
"It obviously was a terrible blow to the organization, a terrible blow to him," MacAloon said. "He helped select many of the members who were found guilty of bribe-taking. ... It will be a lasting footnote to his presidency."
Samaranch used the crisis to push through a package of reforms designed to make the IOC more modern, open and democratic, including a ban on member visits to bid cities.
"We used this crisis to change the structure of the IOC," he said. "Maybe without this crisis, this would not have been possible."
In December 1999, Samaranch became the first IOC president to testify in Congress, enduring three hours of grilling on Capitol Hill from lawmakers skeptical of the reforms.
The 2000 Sydney Olympics, described by Samaranch as the best ever, seemed to take the heat off the IOC and restore faith in the games.
"We showed the world that the Olympic movement after the crisis is even stronger and with even more prestige than before," he said.
Pound said the scandal should not tarnish Samaranch's legacy.
"Once the corner is turned, the progress and the accomplishments in historical terms will supplant the fact that he was on watch when the Salt Lake problem arose," he said.
Samaranch's past was also a target for critics. Jennings and others denounced him for serving the Franco dictatorship in the 1960s and 1970s.
Samaranch angrily defended himself, saying it was up to Spaniards, not foreign journalists, to judge his record. He said he had only a modest role as director general of sports and parliamentary leader of the Falangist movement.
"Maybe some critics pushed me to be president for 21 years," Samaranch said. "I have to thank the critics. Maybe without the critics, I had to leave the IOC before."
Looking back, Samaranch acknowledged he could have retired earlier.
He considered stepping down after the 1992 Olympics in his home city of Barcelona and again after the centennial games in Atlanta in 1996. Each time, encouraged by his supporters, he chose to continue. Twice, he had the age limit changed to allow him to stay on.
As honorary IOC president for life, Samaranch remained active in the Olympic movement even after he stepped down. He chaired the board of the Olympic Museum in Lausanne and regularly attended IOC meetings around the world.
His wife, Maria Teresa, died from cancer in 2000 at 67, shortly after Samaranch presided over the opening ceremony of the Sydney Olympics. Samaranch flew to Barcelona to be at her bedside, but she died while he was still in the air. He later returned to Sydney for the remainder of the games.
In addition to his 50-year-old son, Samaranch is survived by a daughter, Maria Teresa. Both of his children and his partner, Luisa Sallent, were by his side when he passed.
As a youth, Samaranch competed in field hockey, boxing and soccer. He became an IOC member in 1966 and was vice president from 1974-78.
Samaranch served as honorary chairman of La Caixa savings bank in Spain.
"He will have his place in history with Olympism," his son said. "I think he's been very recognized in life and that will only grow with his death."