It shattered coaches and set cars on fire, leaving a trail of bodies including children, as the convoy waited in rebel territory near Aleppo.
There were fears of revenge attacks on evacuees from rebel-held towns, being moved under a deal.
But the exchange later resumed, with coaches reaching safety on both sides.
The "Four Towns" deal brokered by Iran and Qatar was meant to relieve suffering in besieged towns - Foah and Kefraya in the north-west which are under government control, and rebel-held Madaya and Zabadani, near Damascus.
Some 20,000 besieged people would be taken out in all. According to AFP news agency, up to 5,000 government evacuees and 2,200 from rebel towns had been stranded in transit on Sunday.
Last month, the UN described the situation in the besieged towns as "catastrophic". More than 64,000 civilians are "trapped in a cycle of daily violence and deprivation", it said.