The evacuations from the Qabun district in northeast Damascus follow similar departures from the Barzeh and Tishrin neighbourhoods earlier this week.
An AFP correspondent inside Qabun saw around a dozen white buses carrying out residents and fighters in the morning, after a deal for the neighbourhood was announced late Saturday following heavy fighting.
At the edge of the district, two women embraced and wept as they faced the prospect of parting ways.
"I didn't want to leave, but I have to stay with my family, and they prefer to go Idlib after my uncle left with the group from Barzeh," said Suad, wearing a white headscarf and a blue top.
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"I never thought one day I'd be in this position," she added, sobbing heavily.
"I can't describe how I feel."
Those evacuating carried small bags with them as they boarded the buses, while others who had decided to stay registered their names at a military post.
"The Syrian army yesterday managed to encircle dozens of armed elements inside Qabun neighbourhood, forcing them to surrender and hand over their weapons," a source from the pro-regime National Defence Forces militia told AFP.
The signs of the recent fighting, as well as years of prior bombardment and clashes, were visible all around with rubble from partially and completely destroyed buildings strewn across the roads.
Tanks sent up clouds of dusts as they manouevered over the mounds of rubble and dirt and black smoke rose from fires still burning in the neighbourhood.
Others showed off a tunnel they had discovered, one of many that rebels use to connect besieged neighbourhoods.
"This tunnel is ten metres deep, and connects Qabun with the town of Arbin" in rebel-held Eastern Ghouta, one soldier said. "It was used by militants to smuggle weapons and food."
He said another tunnel had been discovered between the Barzeh and Qabun neighbourhoods and destroyed yesterday.
"It was the width of two cars."
A lieutenant, who declined to give him name, said the capture of Qabun had been months in the making.
"We would not have been able to succeed without controlling the network of tunnels. We found more than 10 tunnels so far, and there are still more."
The deals for Qabun, Barzeh and Tishrin neighbourhoods follow a pattern of agreements under which the rebels agree to surrender in exchange for safe passage to opposition-held territory elsewhere.
The government says the deals are the best way to end the six-year war, but the opposition says it is forced into the agreements by regime bombardment and siege.
All three headed to Idlib province, in northwest Syria.
Damascus has been insulated from some of the worst violence of Syria's war, which has killed over 320,000 people since it began with anti-government protests in March 2011.
But the government has made securing control of the last remaining rebel districts in the capital a key priority.