Some 3,800 soldiers carrying automatic rifles and heavy bags boarded five Navy ships and a Hercules air carrier in the port town of Lhokseumawe, just days after Free Aceh Movement rebels handed over their weapons and disbanded their military wing.
Hundreds of people attended a ceremony marking the completion of disarmament and decommissioning, the most delicate phase of a peace deal signed in August to end the bitter conflict that killed nearly 15,000 people.
"That's it," said military spokesman Lt. Col. Eri Soetiko, as the last of 24,000 security forces slated to leave the province under the accord started pulling out of port. "All of the non-organic troops are gone. We've closed our offices."
Efforts to end the 29-year civil war moved forward after the massive earthquake struck off the coast of Aceh on Dec. 26, 2004, causing a tsunami that left at least 156,000 of the province's people dead or missing and a half million homeless.
The rebels and the military each said they did not want to add to the people's suffering and hammered out an agreement during negotiations in Finland in which both sides made major concessions.
Free Aceh Movement representative Irwandi Yusuf and Pieter Feith, head of the 240-strong European Union peace monitoring mission, were among those who turned up at the port Thursday to send off the troops.
Yusuf said he hoped their departure signaled a permanent end to the fighting that has gripped the province of 4 million people on the northern tip of Sumatra island.
He said his former insurgents were looking forward to taking part in local elections next year.
As part of the peace deal, the rebels agreed to hand over all of their self-declared 840 weapons and, in an about-face, gave up their demand for independence.
The government vowed to withdraw more than half of its nearly 50,000 garrison from Aceh and to give the region limited self-government and control over much of the oil- and gas-rich province's mineral wealth.
So far, the deal has stuck with the help of international peace monitors, who said Thursday the former rebels could now focus on politics instead of war.
"Now GAM can use ballots, not bullets, to fulfill their aspirations," said Feith, referring to the Free Aceh Movement by its Indonesian acronym.
Former fighters have come down from Aceh's forested hills in recent months and several rebel leaders have returned to their homeland after more than 25 years of self-exile.
Some, however, have refused to come back because they are wary the peace deal would collapse and that they would be arrested or killed.
After a 2003 accord fell apart, the Indonesian military kicked out foreign observers and restarted combat operations against the rebels.
But Aceh's military commander, Maj. Gen. Supiadin, on Thursday guaranteed the security of all returning rebels.
"We welcome GAM leaders who want to come home," he said, singling out GAM's top exiled leader in Sweden Hasan Tiro. "We'd consider his presence in Aceh as a commitment for peace."
Aceh's conflict first erupted in 1873 when Dutch colonialists occupied the previously independent sultanate. The Acehnese assisted Indonesia's successful 1945-49 war of independence against the Dutch, but launched a decade-long uprising in the early 1950s — this time against Jakarta's rule.
The current rebellion began in 1976.
Many of the 15,000 people killed in the conflict were civilians caught up in army sweeps of remote villages.
Supiadin apologized Thursday for any atrocities carried out by his men, but said they trying to maintain the unity of the country.