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.