They were to be transported to the opposition stronghold of Idlib province.People waiting in the Ramousah garage heard the blast, and said they feared revenge attacks by pro-government forces. In footage aired on Syrian TV, bodies were strewn outside busses, including fighters.
The evacuation deal was brokered by Qatar, negotiating on behalf of the rebels, and Iran, on behalf of the government, in March.
No group has claimed responsibility for the attack.
Syrian state TV reported that a bomber blew up an explosive-laden vehicle at the site.
The state-run Syrian Arab News Agency reported the convoy continued, and the first buses arrived late Saturday in Aleppo.
"I know nothing of my family". It said he was a militant with al-Qaida-linked groups before joining IS.
A rebel spokesman said the auto with the bomb had been parked in the area and abandoned. Yasser Abdelatif, a media official for Ahrar al-Sham, said about 30 rebel gunmen were killed in the blast.
Now in charge of all of Syria's major urban centers, Damascus holds the upper hand against rebels in the west of the country and has negotiated a slew of other surrender deals from a position of strength.
The White Helmets rescue group said 43 people had been killed and that the death toll was likely to rise.
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Assad holds the military advantage over the opposition in the west of the country thanks to Russia's intervention in 2015, although the insurgents continue to fight back and have made gains in some areas.
The exact reasons for the delay in completing the evacuation deal were also unclear.
While talks often begin with extensive demands from the rebel side, these have been whittled down by repeated government airstrikes, as well as pressure from civilians who blame the rebels in part for prolonging their suffering.
An explosion near a bus convoy waiting to enter the Syrian city of Aleppo killed or wounded several people on Saturday, pro-government media outlets, pro-opposition activists and a monitor reported.
"In northern Syria, residents of Shia minority villages, long besieged by rebels, are leaving", NPR's Alison Meuse reports from Beirut. In doing so, it faces a similar fate to the much larger Darayya, another Damascus suburb, which was depopulated following years of crushing government siege and bombardment last August.
Residents were reduced to hunting rodents and eating the leaves off trees. Photos of children gaunt with hunger shocked the world and gave new urgency to United Nations relief operations in Syria. Another 3,000 people are expected to be bused out of Foua and Kfraya on Friday evening, according to Baghdadi.
Many medical workers, activists and former fighters have refused to redeploy with the military that once shelled their homes.
The explosion came as frustration was already mounting over the stalling evacuation process.
Ahmed Afandar, a resident evacuated from his hometown near Madaya, says dozens of busses carrying children, women and men are not allowed to proceed toward militant-held Idlib as planned. "All these thousands of people are stuck in less than (500 yards)".