A large convoy of buses from the government-held towns of Fuaa and Kafraya reached the edge of the rebel-held transit point of Rashidin outside second city Aleppo, the correspondent said.
The Syrian Observatory for Human Rights confirmed the hard-won evacuation deal was back under way.
"The process has resumed with 3,000 people leaving Fuaa and Kafraya at dawn and nearly 300 leaving Zabadani and two other rebel-held areas," the head of the Britain-based monitoring group, Rami Abdel Rahman, told AFP.
Rashidin was the scene of Saturday's deadly car bombing. At least 109 of the 126 dead were evacuees, among them 68 children. The rest were aid workers and rebels guarding the convoy.
Dozens of wounded were taken to hospitals in nearby rebel-held territory, while others were taken to Aleppo, which government forces regained full control of late last year.
Security was tightened up for Wednesday's departures. Several dozen armed rebel fighters stood guard over the marshalling area where the buses were parked.
The AFP correspondent said all other vehicles were carefully searched.
The evacuations were taking place under a deal between the government and the rebels that is also seeing residents and rebels transported out of Madaya and Zabadani, towns near Damascus that are surrounded by pro-government forces.
It was brokered late last month by Qatar, a longtime supporter of the rebels, and Iran, a key regime ally, but its implementation had been repeatedly delayed.
When Wednesday's evacuations are complete, a total of 8,000 people should have left Fuaa and Kafraya, including pro-government fighters as well as civilians.
In exchange, 2,500 civilians and rebel fighters should have left rebel areas including Zabadani and Madaya.
- Second stage to come -
It is the first stage of the deal. A second phase is due to begin in two months' time which should see the two government-held towns entirely emptied and all fighters, and civilians who choose to, leave the two rebel-held towns.
In total that will amount to more than 30,000 people.
The agreement is the latest in a string of such deals, which the government of President Bashar al-Assad says are the best way to end the violence after more than six years of civil war.
Rebels say they amount to forced relocation after years of bombardment and siege.
There was no immediate claim of responsibility for Saturday's bombing.
The government blamed "terrorists" -- a catch-all term for its opponents.
The United Nations says 4.72 million Syrians are in hard-to-reach areas, including 600,000 people under siege, mostly by the Syrian army, but also by rebels or the Islamic State group.
There has been a series of evacuations in recent months, mostly around the capital Damascus but also from the last rebel-held district of Syria's third city Homs.
The civil war has killed more than 320,000 people since it began with anti-government protests in March 2011. More than half of the population have been forced from their homes.