There has been no immediate claim of responsibility for the attack, while the United Nations has demanded that those responsible be brought to justice.
The undamaged buses from the convoy continued Saturday and arrived in the evening at a temporary housing center in the Jebrin area of Aleppo. Once they are out, both towns will be completely emptied of their populations, and the rebels will take over, after besieging the towns for years. Ambulances later took the wounded to hospital in Aleppo.
The contentious transfer of the population, hammered out after rebels lost control of Aleppo in December, stalled overnight as the government and rebels argued over who should be evacuated.
Ahrar al-Sham, the rebel group that negotiated the deal, denounced the "cowardly" attack, saying a number of opposition fighters as well as government supporters were killed in the attack.
Rebels and residents of Madaya meanwhile waited at the government-held Ramousah bus garage, a few miles away. From there they will travel to Idlib province, an opposition stronghold. Now those being moved from other besieged areas fear revenge attacks. They circulated a statement on social media imploring "international organizations" to intervene so the situation did not escalate.
The process of evacuating thousands of civilians and fighters from besieged parts of Syria - in line with an earlier agreement between Bashar al-Assad's regime and opposition forces - was completed late Saturday, according to Anadolu Agency correspondents on the ground.
A wounded girl, who said she lost her four siblings in the blast, told Al-Manar TV from her hospital bed that children who had been deprived of food for years in the two villages were approached by a man in the vehicle who told them to come and eat potato chips.
The agreements are also causing demographic changes, they say, because those who are displaced are mostly Sunni Muslims.
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According to Abdul Hakim Baghdadi, an interlocutor who helped the government negotiate the evacuations, 140 were killed in the attack.
The reasons for the delay were not immediately clear.
Numerous residents still waiting for evacuation now fear reprisal attacks. "My house, land and belongings are all in al-Foua", Mehdi Tahhan said.
"More than 60 children reportedly killed in an attack on a bus convoy yesterday outside Aleppo".
"There's no drinking water or food".
"We're sad and angry about what has happened", he said.
But after the deadly bombing, the rebels apparently succumbed to the pressure of their regional backers and allowed the buses to proceed to the government-controlled Aleppo city, thus marking the implementation of the first part of the deal. Assad's Alawite religious minority is often considered an offshoot of Shi'ite Islam. It is the deadliest such incident in Syria in almost a year.