Jones, of Stansbury Park, died just before midnight Wednesday -- about 28 hours after getting wedged in a tight, unmapped passage with his head at an angle below his feet. Workers had tried feverishly to free him from the shaft about 100 feet below the surface and about 400 feet from the cave's entrance.
Jones was trapped in a vertical shaft about 18 inches wide and 10 inches high within the 1,500-foot Nutty Putty cave, located about 80 miles south of Salt Lake City.
A "Herculean effort" to free him was limited by the cramped space, leaving one rescuer chipping away rock with a ball-peen hammer just six inches to swing, said Sgt. Tom Hodgson, coordinator for Utah County's search and rescue operations.
Sheriff Jim Tracy said Jones' exact cause of death will probably never be known but contributing factors likely included his inverted position for a prolonged period of time and the cave's cold temperatures.
"If we put other people in that same location, they could get stuck or get hurt," said Lt. John Valentine, also of the county's search and rescue.
Those who met Friday morning -- state officials from the agency that owns the land, the cave's operators, Jones' family and law enforcement officials -- said they decided unanimously to close the cave as quickly as possible.
"We feel like it would be John's will to protect the safety of future cavers," his younger brother, Josh, said at a news conference Friday.
Hodgson said "we've suffered a tragedy in this cave that we hope to prevent from happening again."
The family will be allowed to place a memorial marker at the cave.
For the past two years, the St. George native was attending medical school at the University of Virginia, hoping to pursue a career as a pediatric cardiologist. Jones, his wife Emily and their 13-month-old daughter had come home to Utah for the Thanksgiving holiday and to share the news that another baby is expected in June.
Family said they knew Jones fought to survive throughout the rescue effort and was commended by rescue crews for "his remarkable good spirits and resilience to the end."
Although Jones' death is the first known fatality since cavers began exploring Nutty Putty's narrow passageways in the 1960s, rescuers have been called to the cave five times in the last 10 years.
The last time was in 2004 when a teenage boy had to be pulled out of an area not far from where Jones got stuck.
The cave hosted 5,000 to 10,000 visitors per year until 2006, when it was temporarily closed while managers implemented a stricter system of access that included a permit system, requirement that cavers be with someone experienced and a locked gate. It reopened in May and had once again become popular, especially among amateur cavers, said Mike Leavitt, who managed access to the cave.
Although the cave was popular, it had never been fully mapped. Jones found himself in one of the areas off the cave's main passage during an outing with 11 friends and family Tuesday night and was unable to get out.
"This particular area is very, very difficult ... where the cave peters out to virtually nothing," said Valentine, who said he'd been in Nutty Putty some 25 times over the years.
Funeral services for Jones are planned for Saturday. Josh Jones said the family is considering a fund to help educate young people on cave safety.