Some 3,000 people have left the north-western villages of Foah and Kefraya, which have been surrounded by rebels.
Meanwhile, buses have moved dozens of others from Zabadani, near Damascus, under siege by pro-government forces.
Security has been tight after Saturday's attack near Aleppo.
The evacuations resumed early on Wednesday, the UK-based Syrian Observatory for Human Rights monitoring group said.
At the Rashidin checkpoint, where the handover of evacuees was due to take place, buses were being carefully searched after the bombing there, an AFP correspondent at the scene reported.
Several dozen armed rebel fighters stood guard near the convoy.
Um Joud, 55, was part of those being evacuated from Foah. "I'm not afraid, because everything is in God's hands," she told AFP.
"Of course I would have preferred to stay in my home, but I left for the sake of my children and their lives and futures."
Last week's attack was caused by a vehicle filled with explosives which targeted a convoy of buses at the checkpoint.
Most of the killed were evacuees from government-held towns, including at least 68 children. No group has said it was behind the attack.
Wednesday's evacuations mark the end of the first stage of the deal, with a second phase due to begin in June, AFP reports.
Opposition-controlled Zabadani and Madaya were now "empty" of militants, said Mayyada al-Aswad, a member of the co-ordinating committee on the government side.
More than 30,000 people are expected to be moved under the deal to end a grave humanitarian crisis.
Last month, the UN described the situation in the four towns as "catastrophic", with more than 64,000 civilians "trapped in a cycle of daily violence and deprivation".
Many people are reported to have died as a result of shortages of food or medicine.
Some 4.7 million people live in hard-to-reach and besieged areas in Syria, including 644,000 in UN-declared besieged locations.
Meanwhile, a bomb explosion killed at least six people and injured 32 others in Aleppo's Salah al-Din district, state TV reported, without providing details.
The area was under rebel control before pro-government forces took the entire city last December.
Evacuations from two government-held areas of Syria have resumed, monitors and reports say, days after an attack on a convoy carrying evacuees killed 126 people, many of them children.