The French rock star, who died of lung cancer on Wednesday aged 74, had asked to be laid to rest there in a choice that has disappointed some fans who would have preferred his grave to be more accessible on the mainland.
Hundreds of thousands of people lined the streets of Paris on Saturday to watch his white coffin, escorted by some 700 bikers, travel down the Champs Elysees in what was a state funeral in all but name.
The coffin left Paris on Sunday morning on a Boeing 757 with 62 passengers onboard, including his wife Laeticia and their two children who will lead a private burial ceremony on Monday.
Around a dozen fans were at the airport as the plane took off.
"I wanted to be with him right to the end because he always gave everything," 54-year-old veteran fan Fred Bouton told the AFP news agency.
Bouton said he had already started looking up air tickets for the eight-hour trip to St Barts which are often in excess of 1,000 euros.