The 3,000 evacuees, who had left their homes at dawn yesterday, spent the night in buses in a marshalling area in Rashidin, west of government-held second city Aleppo, awaiting onward transport to safety.
Some 300 evacuees from rebel-held towns were similarly held up at a staging point at Ramussa in government-held territory.
The Syrian Observatory for Human Rights said the delay was the result of 11th-hour rebel demands for the release of prisoners held by the government.
The hard-won resumption of evacuations on Wednesday came after a suicide car bomber killed 126 people, 68 of them children, in Rashidin on Saturday.
Most of the dead were evacuees from the government-held Shiite-majority towns of Fuaa and Kafraya, with a handful of aid workers and rebels guarding the convoy also killed.
Armed rebels were standing guard at Rashidin on Wednesday and carefully inspecting vehicles arriving in the area.
Fuaa and Kafraya will be emptied entirely, with residents and fighters heading to Aleppo and then on to government-held Latakia or Damascus.
All rebels are expected to leave Madaya, Zabadani, and other nearby oppositions-held areas, but civilians who want to remain may do so.
Those leaving rebel-held areas will head to Idlib province, which is held by an opposition alliance.
In all, up to 30,000 people are expected to leave under the deal.
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