The agreement had stalled, leaving thousands of people from both government-besieged and rebel-besieged areas stranded at two transit points on the city's outskirts, before the explosion occurred.
Late on Saturday buses began crossing into both government-held and rebel-held territory from the two transit points as the deal resumed, pro-Damascus media and the Syrian Observatory for Human Rights monitoring group reported.
But the incident underscored the difficulty carrying out any agreement between warring sides in a volatile and complex Syrian conflict which, in its seventh year, shows no signs of easing.
A media unit run by Damascus ally Hezbollah said the attack was carried out by a suicide car bomb and killed at least 100 people. The Observatory said more than 24 were killed and scores more wounded.
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Residents, fighters evacuate from four besieged Syria towns
Footage on state TV showed bodies lying next to charred buses with their windows blown out, and vehicles in flames.
The blast hit buses in the Rashidin area on Aleppo's outskirts. The vehicles had been waiting since Friday to cross from rebel-held territory into the government-controlled city itself. Ambulances later took the wounded to hospital in Aleppo.
The convoy was carrying residents and pro-government fighters from the Shi'ite villages of al-Foua and Kefraya, which are besieged by rebels in nearby Idlib province, an insurgent stronghold.
They had left under a deal where, in exchange, hundreds of Sunni insurgents and their families were granted safe passage from Madaya, a government-besieged town near Damascus.
But a delay in the agreement had left all those evacuated stuck at transit points on Aleppo's outskirts since late on Friday.
Residents of al-Foua and Kefraya waited in the Rashidin area.
WATCH: Syrian evacuate in their thousands
Rebels and residents of Madaya meanwhile waited at the government-held Ramousah bus garage, a few miles away. They were to be transported to Idlib.
People waiting in the Ramousah garage heard the blast, and said they feared revenge attacks by pro-government forces. They circulated a statement on social media imploring "international organizations" to intervene so the situation did not escalate.
The evacuation deal is one of several over recent months that has seen President Bashar al-Assad's government take back control of areas long besieged by his forces and their allies.
The deals are unpopular with the Syrian opposition, who say they amount to forced displacement of Assad's opponents from Syria's main urban centers in the west of the country.
They are also causing demographic changes because those who are displaced are usually Sunni Muslims, like most of the opposition. Assad is from the minority Alawite sect and is supported by Shi'ite regional allies.
A handout photo made available by Thiqa News Agency (TNA) showing rescue and media personnel at the scene of a car bomb attack (AAP) Source: AAP
It was unclear who carried out Saturday's bombing attack.
The exact reasons for the delay in completing the evacuation deal were also unclear.
'Forced displacement'
The Observatory said the delay was caused by the fact that rebels from Zabadani, another town near Damascus included in the deal, had not yet been granted safe passage out.
A pro-opposition activist said insurgents blamed the delay partly on the fact that a smaller number of pro-government fighters had left the Shi'ite villages than was agreed.
Earlier on Saturday, at the transit point where the buses from al-Foua and Kefraya were waiting, one resident said he was not yet sure where he would live.
"After Aleppo I'll see what the rest of the group is doing, if there are any preparations. My house, land and belongings are all in al-Foua," Mehdi Tahhan said.
A Madaya resident, speaking from the bus garage inside Aleppo, said people had been waiting there since late on Friday, and were not being allowed to leave.
"There's no drinking water or food. The bus garage is small so there's not much space to move around," Ahmed, 24, said.
"We're sad and angry about what has happened," he said. Many people felt that they had been forced to leave," he said.
"There was no other choice in the end - we were besieged inside a small area in Madaya."
Other evacuation deals in recent months have included areas of Aleppo and a district in the city of Homs.
Syria's population is mostly Sunni. Assad's Alawite religious minority is often considered an offshoot of Shi'ite Islam.
He has been backed militarily by Russia, and by Shi'ite fighters from Iran and the Lebanese Hezbollah group in Syria's six-year-old conflict.
Assad has the military advantage over rebels in the west thanks to Russia's intervention in 2015, although the insurgents are still fighting back and have made gains in some areas.
