A source close to the deal confirmed the arrival of over 300 people from the government-controlled towns of Fuaa and Kafraya in northwestern Idlib province to the Sayyida Zeinab area south of the capital.
An official celebration to welcome the arrivals was expected later Tuesday, the source said.
The 338 people were evacuated in deal that saw over 450 fighters and civilians, including the wounded, leave three flashpoint areas in Syria as part of a six-month truce reached in September.
The residents and fighters from Fuaa and Kafraya were evacuated to Turkey, flown to Beirut, and then driven into Syria.
The two villages are under rebel siege.
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At the same time, some 126 people from the rebel stronghold of Zabadani near the Lebanese border, which is surrounded by government forces, were evacuated to Beirut for transfer to Turkey.
From Turkey they were to travel on to rebel-held areas in northern Syria.
The evacuation was facilitated by the UN, the International Committee of the Red Cross (ICRC) and the Syrian Arab Red Crescent, which in a statement Monday urged the implementation of the rest of the deal, including the delivery of aid.
Tareq Wheibi, an ICRC spokesman, said limited aid had been delivered during the operations on Monday, but that more was needed.
"Yesterday we were able to deliver some aid, just some food and water, nothing really substantial," he told AFP.
"A lot more needs to be done and we're hoping this would happen in the next week. We're waiting for the green light."