Five buses carrying rebels and their relatives from towns near the capital left a transit point outside Aleppo city where they had been waiting to cross into rebel territory, the state-owned news channel Ikhbariyah said.
Meanwhile, ten busloads of people from the rebel-encircled Shi'ite towns of al-Foua and Kefraya arrived in Aleppo city, which is under government control, al-Ikhbariyah said.
Thousands of evacuees from the two Shi'ite towns have been stranded for two days at a second nearby staging area outside Aleppo, where a bomb attack on an evacuation convoy last week killed scores of people.
The Syrian Observatory for Human Rights said the 48-hour suspension was due to rebel demands for the government to free 750 prisoners as part of the agreement.
The Britain-based war monitor confirmed the resumption on Friday morning of evacuations under the reciprocal deal, but said it remained unclear if authorities had released the prisoners.
Under the deal, thousands of Sunni rebels and civilians have been moved out of Zabadani and Madaya, which have long been under siege by pro-government forces. They departed for rebel-held Idlib, bringing the two towns near Damascus under state control.
In exchange, thousands of civilians and pro-government fighters were moved out of al-Foua and Kefraya, besieged by insurgent groups in Idlib in northwest Syria.
On Saturday, a bomb blast hit a convoy carrying evacuees from al-Foua and Kefraya killing at least 126 people, including more than 60 children, who were waiting on Aleppo's outskirts.