Syrian troops responded by driving the jihadists from the Sukkari district with the aid of Russian aid strikes and penning them into Salaheddine and Sayf al-Dawla, a combined area of less than one square mile.
Rebel shelling in return killed six civilians in government-held areas of the city and injured dozens more.
The deal struck between Russia and Turkey on Tuesday unravelled while the remaining militants and their families were set to be taken to a town north-east of the city at 5am.
Buses brought in to transport 5,000 people were pulled back after militants allegedly fired on them.
The pro-government al-Masdar news agency claimed the numbers exceeded 15,000, including 4,000 gunmen mostly from the al-Qaida-linked Levant Conquest Front.
But a government source said no full agreement on Aleppo could be reached without addressing the situation on other fronts.
Turkish President Recep Tayyip Erdogan rushed to blame the Syrian government, claiming: “Not even a few hours had passed since the agreement was reached that the regime forces broke the ceasefire and once again started to attack civilians.”
A last-ditch attempt by insurgents outside the city to break through into the north-western Zahra suburb using multiple suicide vehicle bombs failed on Tuesday.
At Tuesday night’s emergency UN security council debate, US ambassador Samantha Power claimed Syria, Russia and their ally Iran were “behind the conquest of and carnage in Aleppo,” while Britain’s Matthew Rycroft alleged that “every single law of war has been broken by the regime.”
But Syrian UN ambassador Bashar al-Jaafari insisted: “Aleppo has been liberated from terrorists and those who toyed with terrorism. Aleppo has returned to the nation.”
Russian Defence Minster Sergey Lavrov said yesterday that Western demands for a ceasefire were just a ploy to give the militants time to regroup.
“No-one in Iraq, in Libya or especially Yemen insists on immediately halting armed activities and observing a week or two of full silence before sitting down at the negotiating table, but they do so in Syria,” he said.