Dozens of people, many of them in military-style uniforms, ran alongside two limousines and an ambulance carrying Arafat and his aides to the helicopters.
Amid a crush of chanting supporters the 75-year-old was carried on to the helicopter, accompanied by his wife Suha and a team of medical staff and advisors.
Overnight, Palestinian bulldozers had cleared a makeshift landing area for the helicopters by moving aside wrecked cars and rubble.
Later Arafat’s helicopter landed at a military airport in eastern Amman, where a throng of well wishers lead by Jordanian Foreign Minister Hani Mulki awaited him before he boarded the Paris-bound plane.
French and Arab diplomats and Palestinian officials, including foreign minister Nabil Shaath, also gathered at the airport under a fine drizzle to bid farewell to the 75-year-old Palestinian leader,
It is the first time that Yasser Arafat, icon of the Palestinian struggle for statehood, has left the Palestinian territories in nearly three years.
He has been effectively kept under house arrest at his Ramallah compound by Israeli troops.
However, Israel, which has declared Arafat an obstacle to peace, has indicated that it will allow the Palestinian leader to return to Ramallah after treatment.
Doctors suspect that the 75-year-old leader, who has been sick for two weeks, may be suffering from leukaemia.
His slide into illness has raised fears of chaos among Palestinians, whose four-year-old uprising for a state has stalled.
However Arafat’s top advisor, Nabil Abu Rudeina, said Arafat’s absence would not lead to any leadership vacuum.
“The prime minister and rest of the leadership will be functioning as usual. Everything will go fine, there’s no vacuum.”
Earlier French President Jacques Chirac sent a get-well message to the man who has come to symbolise the Palestinian struggle for independence.
“France, as you know, backs the aspiration you embody for the creation of a viable, prosperous and peaceful Palestinian state alongside a state of Israel assured of its security,” the president wrote.
And in Washington, State Department spokesman Richard Boucher said the US administration hoped the Palestinian Authority chief would “get the medical care that he needs to return to health”.