For more than two years, the government of President Bashar al-Assad has touted such "reconciliation deals" as the best way to end the country's brutal war.
Today's evacuations were part of the first such deal for the Syrian capital itself.
According to Syrian state news agency SANA, 718 rebels were among a total of 1,246 people evacuated from the Damascus districts of Barzeh and Tishrin.
"The exit of armed fighters and their families will be completed in several waves in the coming days until the district is completely free of any signs of armed people," the agency said.
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A source from the pro-government National Defence Forces confirmed the same number of evacuees from Barzeh and told AFP they left on 12 buses.
"The evacuations are part of the deal reached first in Barzeh, to which the neighbouring northeastern district of Tishrin was later added," the source said.
The Syrian Observatory for Human Rights said that months of negotiations had been held to secure the evacuations of three rebel districts of Damascus: Barzeh, Tishrin and Qabun, also in the northeast.
Talks over Tishrin continued in secret throughout the week until today, according to Observatory head Rami Abdel Rahman.
No deal has yet been reached on Qabun, where government forces yesterday seized control of a number of apartment blocks and a power station, the Observatory said.
Abdel Rahman said the advance was part of efforts to push rebels there to join the evacuation agreement.
Syria's government has announced its intent to include more Damascus neighbourhoods in the deal, among them Qabun and the Palestinian camp of Yarmuk in the south.
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