The burial ended the gruesome spectacle of Gadhafi's decaying corpse on public display in a cold storage locker at a Misrata warehouse for four days after he was killed in his hometown of Sirte on Oct. 20.
The location of the brutal dictator's grave site was not disclosed by the interim government for fear of vandalism by his foes and veneration by his die-hard supporters.
Gadhafi, 69, was buried Tuesday along with his son Muatassim and former Defense Minister Abu Bakr Younis after the military council in the city of Misrata ordered a reluctant Muslim cleric to say the required prayers.
Libya's new leaders hope the funeral will allow the country to turn the page on the four-decade Gadhafi era and the bloody eight-month rebellion against him. Still, the book cannot be closed completely, with unanswered questions remaining about his slaying, and his son and one-time heir apparent, Seif al-Islam, still at large.
Under international pressure to investigate the circumstances of Gadhafi's death, the interim leaders of the National Transitional Council issued a statement late Tuesday saying they "disapprove" of any prisoner being hurt, let alone killed. It was the first time the new leadership spoke out against Gadhafi's killing.
"Regardless of the hatred that Libyans held for Moammar Gadhafi and his regime because of the suffering he inflicted, and how he soiled their reputation for four decades, we did not want to end this tyrant's life before he was brought to court, and before he answered questions that have deprived Libyans from sleep and tormented them for years," the statement said.
The three bodies were moved under cover of darkness late Monday by the city's military council. They were taken from the warehouse area to a school in Misrata where suspected regime loyalists are being held, said Mohammed al-Madani, a Muslim cleric and one of the detainees.
About 1:30 a.m. Tuesday, al-Madani and another detained cleric were ordered to pray over the bodies, which had been wrapped in shrouds, with their faces covered. Al-Madani told The Associated Press that he initially refused, but felt he had no choice and quickly said the required Muslim prayers.
A Gadhafi nephew and two sons of Abu Bakr also participated in the prayer, said Ibrahim Beitalmal, a spokesman for the military council. The nephew was later identified as Abdel Rahman Abdel Hamid, son of a Gadhafi sister and in detention since trying to escape from Sirte in September.
The bodies were then put in coffins, handed over to authorities and driven to another location for burial, which took place at around 5 a.m., according to al-Madani and Beitalmal.
Libya's interim government has said it would not reveal the location of the grave, but a Misrata official, who spoke on condition of anonymity because he was not allowed to disclose details, said the site was in the desert.
Libya's uprising, which began in mid-February and quickly turned into a civil war, has decimated Gadhafi's family. Three sons -- Muatassim, Seif al-Arab and Khamis -- have been killed. Gadhafi's wife, Safiya, fled to Algeria with their daughter Aisha and sons Hannibal and Muhammed.
A senior official in neighboring Niger said Gadhafi's son Seif al-Islam, who is wanted by the International Criminal Court on war crimes charges for his role in trying to crush the uprising, was trying to flee there to join other regime loyalists.
The escape of the Western-educated son, once seen as a likely successor, raised the possibility of attempts to direct an insurgency against Libya's new rulers, though it's not clear if exiled loyalists have the drive, money and support to do so.
Rissa ag Boula, an adviser to Niger's president, said the younger Gadhafi is getting help from ethnic Tuaregs, a tribe that was among Gadhafi's strongest supporters. He said Seif al-Islam appeared to be poised to cross into Algeria in order to make his way to Niger.
It would be the same route that his brother al-Saadi Gadhafi and more than 30 other Gadhafi loyalists had used in September. Al-Saadi Gadhafi -- not wanted by the international court but subject to U.N. sanctions -- is held under house arrest in a gated compound in Niger's capital.
The son of a Bedouin tribesman, Moammar Gadhafi took power in a military coup in 1969 and ruled Libya with an eccentric brutality, turning the country into an isolated pariah, then an oil power courted by the West, and then back again. At home, he imposed his whims on an entire country.
In the final weeks of his life, the mercurial strongman who had given himself grand titles like "king of kings of Africa" lived as a fugitive, sheltering in abandoned homes without electricity, using candles for light and brewing tea on coal stoves, a confidant said.
Gadhafi fled his residential compound in the capital of Tripoli on Aug. 18 or 19, just before revolutionary forces first entered the city, said Mansour Dao, Gadhafi's chief bodyguard, who was captured along with his former boss.
Gadhafi headed straight to his birthplace of Sirte, Dao told the AP, speaking Monday in a conference room -- now serving as a jail cell -- of the Misrata military council.
He said Gadhafi alternated between rage and despair as his regime crumbled. Gadhafi and two-dozen loyalists, including Dao, moved from hideout to hideout about every four days, as anti-Gadhafi forces closed in.
Dao said Gadhafi had underestimated the opposition to his rule and missed the chance to go into exile. The man who once ruled a country of 6 million with an iron fist railed against his lack of power.
"He was stressed, he was really angry, he was mad sometimes. Mostly, he was just sad and angry," Dao said.
"He believed the Libyan people still loved him, even after we told him that Tripoli had been occupied."
Witness accounts and video taken of the deposed dictator after his capture by fighters from Misrata show that he was beaten and abused by his captors, and Peter Bouckaert of the New York-based Human Rights Watch said there are strong indications Gadhafi and Muatassim were killed in custody.
The interim government agreed under mounting international pressure to investigate Gadhafi's death. Rights activists said it's imperative to investigate suspected atrocities and avoid the impression vigilante justice is being condoned.
Gadhafi's body was taken back as a trophy to Misrata, which had been besieged and indiscriminately shelled by his forces for nearly two months during the uprising before they were pushed out in fierce street fighting.
Libya's chief pathologist, Dr. Othman el-Zentani, performed autopsies on Gadhafi, Muatassim and Abu Bakr and took DNA samples to confirm their identities. El-Zentani has said Gadhafi died from a shot to the head and said the full report would be released in coming days, after he presents his findings to the attorney general.
Government officials have suggested Gadhafi was killed in crossfire.
However, Bouckaert said Gadhafi and Muatassim were not fatally injured when they were captured. He said he believed the fatal shots were fired after the two were already in custody.
"It has nothing to do with crossfire," he said. "They were killed while in detention."
In the NTC statement issued after the burial, Oil and Finance Minister Ali Tarhouni said that the interim government would have preferred that Gadhafi stand trial.
The statement listed more than a dozen questions the NTC said it wanted Gadhafi to answer, including his justification for the bombing in 1988 of a Pan Am jetliner over Lockerbie, Scotland, and why he denied thousands of Libyan political prisoners due process in the legal system.
Tarhouni also promised that fair trials would be guaranteed for Libyans suspected of committing war crimes or criminal acts, including any who allegedly killed Gadhafi.
The interim government faces other allegations that revolutionary fighters were involved in atrocities. Earlier this week, Human Rights Watch discovered 53 decomposing bodies, apparently of Gadhafi loyalists, some with hands tied behind their backs, in what appeared to be a massacre of prisoners by revolutionary forces in Sirte.