The couple received an urn with his ashes and left the island chain on Monday night, according to Obie Wilchcombe, a member of the Bahamas parliament and a family friend.
"Everything was in place, the cremation was completed, and they decided to leave," Wilchcombe told The Associated Press on Tuesday. He said the family is back in Ocala, Florida, where they have a home.
For years, Jett Travolta suffered profound seizures. So what caused his death - according to the mortuary director - was not surprising:
"The cause of death was seizure disorder," said Keith McSweeney of Restview Memorial Mortuary and Crematorium.
But how did it happen - and, especially, why? For the close-knit Travoltas, there are no ready answers, certainly nothing an autopsy could explain.
John Travolta and Preston, have said Jett became very sick when he was two years old and was diagnosed with Kawasaki Syndrome, an illness that leads to inflamed blood vessels in young children.
Preston blamed household cleaners and fertilizers for his illness and said that a detoxification program based on teachings from the Church of Scientology helped improve his health.
Jett was found unconscious in a bathroom on Friday at the family's vacation home on Grand Bahama Island.
At the Rand Memorial Hospital in Freeport Monday, a pair of forensic pathologists examined Jett's body for two hours. The autopsy revealed there were no signs of head trauma, reports CBS News correspondent Mark Strassmann.
The assistant director of the funeral home told The Associated Press that the body had minimal injuries despite police officials who had said the teen hit his head on a bathtub.
Authorities didn't release the results of an autopsy performed Monday, but the assistant director of the funeral home saw the body and the death certificate, which was based on its findings.
He added that the only cause of death listed was seizure.
Jett's remains were then cremated.
"Very difficult day, obviously," said Wilchombe. "It's been a very difficult time for the Travoltas ever since Friday. And it continues."
What may never be clear: how much time passed before someone found him unconscious on a bathroom floor in the family's home in this posh resort.
Appearing on CBS' The Early Show, leading forensic pathologist Cyril Wecht, M.D., J.D., characterized the findings as "really completely negative. The autopsy revealed no other cause of death such as a congenital heart condition or a stroke with hemorrhage into the brain.
"You cannot see evidence of a convulsion," Wecht said. "The convulsive seizure disorder disrupts the brain, literally shakes, seizes it, [and] the neural pathways from the brain that control the heart and lungs are disrupted. That leads to a cardiac dysrhythmia, and they go into cardiac arrest."
Wecht said that when someone suffers from that kind of disorder, intervention must be immediate. "You have to find out if someone is going into a convulsive seizure or act immediately upon visualizing it, to see to it that an airway is established, that oxygen is administered, and that the heart is kept going in an artifactual fashion until the brain's seizure activities have subsided.
"So that's the tragedy here. They found nothing, in other words, and they're going based upon the clinical history, I think it is a correct diagnosis."
Wecht thinks that the fall Jett was reported to have taken in the bathroom, hitting his head, did not contribute to his death.
Usmagazine.com reported that Travolta tried CPR (Cardiopulmonary resuscitation) to revive his son, who may have died in his arms before an emergency medical technician took over. Us cited Travolta's attorneys Michael McDermott and Michael Ossi.
Wecht told The Early Show that microscopic study of tissues might be able to suggest whether or not Jett could have been saved if help had come sooner. "But I predict that that will never be disclosed. In other words, they will see how much fluid has built up in the lungs and how much congestion there is back into the spleen and liver. In determining that, they can try, then, to correlate the time situation.
"But grossly, they cannot tell too much. And this is the kind of a finding, I'm sure, that the family is not going to share with anybody."
In a public statement released on Sunday, John Travolta and wife Kelly Preston said they were "heartbroken that our time with him was so brief."
Jett's death hits hard on this island the Travoltas have called their vacation home for the last six years. Many locals consider them extended family.
So when the teen died, Wilchombe said, "We felt the pain. It's like we've lost a family member."
Late Monday, a black hearse traveled from the funeral home to the airport after the family indicated they were bringing Jett's remains to Ocala, Florida, where they own a home.
But the hearse was dispatched as a ruse, McSweeney told a news conference later Monday.
On their private plane, the Travoltas had flown about sixty guests to the Bahama's West End for their annual New Year's island celebration.
Many of them will go back with the family to Florida, to end a trip in a way no one could have imagined: with a final goodbye to the son of their host.