After a good-bye lunch with his mother, Mr. Zelaya, his wife and his daughter left their refuge in the Brazilian Embassy and headed for the airport. They were accompanied by the new president, Porfirio Lobo, along with President Leonel Fernandez of the Dominican Republic, who last week invited Mr. Zelaya to the Dominican capital, Santo Domingo, last week.

The usually voluble Mr. Zelaya said little to the thousands of supporters who had been waiting for hours to see him off, but the group promised to return as it boarded Mr. Fernandez’s plane. On arrival in Santo Domingo, Mr. Zelaya thanked Mr. Fernández and called on Mr. Lobo to continue taking steps to restore democracy.

His departure on the day of Mr. Lobo’s inauguration pointed toward an end to the protracted political crisis that has gripped Honduras since the June 28 coup that ousted Mr. Zelaya.

But the country remains sharply divided between those who support the coup — because they resented Mr. Zelaya’s leftward tilt and feared he was trying to extend his tenure — and those who continue to back him as a defender of the poor. The new government may also face challenges to its legitimacy, since many nations refused to recognize the elections that brought Mr. Lobo to power.

Mr. Lobo, a wealthy conservative who lost the 2006 election to Mr. Zelaya, stopped only a few minutes into his inaugural speech Wednesday to sign an amnesty decree approved by Congress late Tuesday. He also announced that he would set up a truth commission to study the events that led to the coup and its aftermath.

“We are emerging from the worst political crisis in our history,” Mr. Lobo said to a crowd at the national stadium in the Honduran capital, Tegucialpa.

The amnesty lifts the abuse of power charges that had hung over Mr. Zelaya, but he still faces allegations of embezzling funds. The amnesty also protects those who orchestrated the coup.

Mr. Zelaya’s ouster brought worldwide condemnation and repeated calls by governments, including the Obama administration, for his return. No country recognized the government that took power after the coup.

In a region where the shadow of past coups still falls over weak democracies, the image of Honduran soldiers arresting and expelling an elected president raised fears that it would embolden militaries in other countries.

But the de facto government withstood the pressure, and went ahead with elections scheduled long before the coup. Mediation efforts, first by the Costa Rican president, Óscar Arias, and then by the State Department, failed to budge the de facto president, Roberto Micheletti.

After three months in exile, Mr. Zelaya slipped back into the country, where he sought protection from arrest in the Brazilian Embassy. He had remained there since September, talking on the phone to the media, supporters and negotiators, strumming his guitar and playing chess to pass the time.

The political impasse cost the economy $2 billion in lost aid and investment, Mr. Lobo said. One of his first tasks, he added, would be to win international approval for his new government.

He also thanked Mr. Arias and Secretary of State Hillary Rodham Clinton, among others, for trying to find a way out of the crisis. The mention of their names, however, brought boos from the crowd, a sign of resentment over outside interference.

Mr. Micheletti, who was hailed by his supporters as a protector of democracy, was named legislator for life by the Congress several weeks ago.