(AP Photo/Arnulfo Franco)
The leftist leader drove past soldiers guarding the diplomatic compound in long caravan and headed for the airport accompanied by President Porfirio Lobo, said Hilda Cruz, an assistant of Zelaya's wife.
Zelaya was going to the Dominican Republic as a private citizen under a deal signed by Lobo and the Caribbean country's President Leonel Fernandez, who flew to Honduras to accompany the former president.
Zelaya has not elaborated on plans for his future. But just before boarding the plane, he shouted: "We'll be back! We'll be back!"
Thousands of supporters gathered outside the airport yelled "Mel, our friend, the people are with you!" as his plane took off.
Lobo, who was sworn into office hours earlier, had said his first task as president would be providing Zelaya a safe passage out of the country.
"We have emerged from the worst crisis in the democratic history of Honduras," said Lobo, 61. "We want national reconciliation to extend to a necessary and indispensable reconciliation with the international community."
Zelaya, who was ousted in a dispute over changing the Honduran Constitution, insisted he was still president up until the moment his four-year constitutional term officially ended Wednesday.
Zelaya left with his wife, two children and an aide after four months holed up in the embassy. The couple had their hair done by a stylist, packed five suitcases and said they were taking Zelaya's guitar and Christmas cards from supporters.
It was a quiet end to his tumultuous struggle to return to power after soldiers stormed his residence and flew him out of the country in his pajamas.
"He's done. I think at this point, if you are Zelaya, you slink away into the corner and you recoup for a little while," said Heather Berkman, a Honduras expert with the New York-based Eurasia Group. "But I think in the near term, Zelaya is finished as a politician."
The country's institutions moved quickly this week to try to leave the coup behind.
A Supreme Court judge found six generals innocent of abuse of power charges for ordering soldiers to hustle Zelaya out of the country at gunpoint. And Congress voted to approve amnesty for both the military and Zelaya, who had been charged with abuse of power and treason over his defiance of a Supreme Court order to cancel a referendum on changing the constitution.
He remains under investigation for embezzlement in connection with $1.5 million in government funds.
Opponents said Zelaya wanted to hold onto power by lifting a ban on presidential re-election, as his ally Venezuelan President Hugo Chavez did. Zelaya denies that and says he only wanted to give more voice to Honduras' many poor and shake up a stagnant political system dominated by a few wealthy families.
Zelaya slipped back into Honduras in September, hiding in the trunk of a car. He turned up at the Brazilian Embassy to the dismay of interim President Roberto Micheletti and the delight of hundreds of supporters who followed the ousted leader into the diplomatic mission and vowed not to leave until he was restored to power.
As U.S.-brokered talks dragged on and ultimately failed to reverse the coup, the supporters slowly went home. Zelaya left behind a plastic chess set someone gave him to help pass time. His family snapped photos to remember their time there.
"This is a moment of much happiness because we are leaving the confinement we've been in for 129 days, but also of sadness because we are leaving our people, who have always accompanied us, and our land," Zelaya's wife, Xiomara Castro, told Radio Globo from the airport. "But we'll be back and we'll fight for our Honduras as long as we breathe."
An aide has said Zelaya will likely take up residence in Mexico.
Micheletti bet that international pressure for Zelaya's return would fade after Nov. 29 presidential election, which were scheduled before the coup. It largely worked.
Lobo said the U.S. government has assured him that it would restore millions of dollars in aid and the World Bank has indicated it would consider lifting a block on credit.
However, Arturo Valenzuela, the assistant U.S. secretary of state for Western Hemisphere affairs, said the United States has made no decision on restoring the aid. He said it was important Honduras meet several requirements of a U.S.-brokered pact signed by Zelaya and Micheletti, including the creation of a truth commision to investigate the events that led to the coup.
Valenzuela, who was in Honduras for the inauguration, said he was confident Lobo would quickly move to meet those requirements.
"If these steps are taken we're going to evaluate our positions," Valenzuela said in a conference call with reporters. "We're please to see that the new president of Honduras is taking the country in the right direction.
Some left-led Latin American countries, including Brazil and Venezuela, insisted that recognizing the election outcome would amount to condoning a coup in a region that has long struggled to install stable democracies.
But El Salvador promised to restore ties and Brazil indicated it might do the same.
"I think the way President Zelaya and those he represents are treated in the future will tell us if we are on a good path or not," Brazilian Foreign Minister Celso Amorin told the state news agency.
Associated Press writer Juan Carlos LLorca reported in Tegucigalpa, and Alexandra Olson in Mexico City.