His coffin, draped in the Palestinian flag, was taken to a military airport, where a ceremony attended by members of the French government was held.
The plane carrying his body then took off for Cairo, where his funeral will be held on Friday.
The Palestinian Authority has declared 40 days of mourning.
Mr Arafat's widow Suha wept openly with her head bowed during the ceremony at the Villacoublay airport.
She was accompanied by French Prime Minister Jean-Pierre Raffarin and Palestinian Foreign Minister Nabil Shaath.
As a military band played a funeral march, Mr Arafat's coffin was carried by a guard of honour to an Airbus plane bearing the livery of the French republic.
The BBC's Caroline Wyatt in Paris described the ceremony as simple but dignified - a send-off fit for a head of state, as many in France saw Mr Arafat.
No members of the public were present at the airport. Earlier, crowds of Arafat supporters at Percy hospital, chanting, "We are all Palestinians", had waved candles and flags as Mr Arafat's body began its journey home.
Somewhat sickening. Of course, "We are all Palestinians," means solidarity against the evil oppressor jew.
Some militants accused Israel of causing his death and a leader of Al-Aqsa Martyrs Brigades, Raid al-Aidi, swore to avenge it:
"We hold Israel fully responsible for the assassination of our mentor and father... It was caused by the siege imposed on him."