At least 71 bodies were found by a river in the western Bustan al-Qasr district, UK-based Syrian Observatory for Human Rights (SOHR) said.
Most had their hands tied behind their backs and gunshot wounds to the head.
Hours after the find, UN envoy Lakhdar Brahimi reportedly said Syria was “breaking up before everyone’s eyes”.
He told a closed-door session of the UN Security Council that he had no progress to report, adding that the government’s legitimacy had been “seriously, probably irreparably, damaged”, diplomats said.
Mr Brahimi has been trying to seek a way out of the crisis on the basis of a peace plan approved at an international conference in June 2012.
The UN says the conflict has left more than 60,000 people dead.
Shot in the head
Video footage of the gruesome discovery was posted by activists on YouTube.
It showed a large number of bodies strewn in and around the banks of the Quwaiq river, which skirts the western side of Aleppo.
The bodies were caked in grey mud and showed signs of rigor mortis. There were also signs of blood having poured from many of the heads.
Rigor mortis, a stiffening of the limbs of a corpse, begins around three hours after death, peaks at around 12 hours and is completely dissipated some two days later.
Daily Telegraph correspondent Ruth Sherlock, who was at the scene, told the BBC there was “absolute pandemonium”.
“There were pickup trucks outside with people standing crying, screaming over corpses that were being taken away,” she said.
Sherlock said she counted at least 71 bodies in different stages of decomposition, mostly between the ages of 20 and 40, as well as two boys aged about 11 and 15.
One volunteer helping to load bodies on to a lorry said there was no identification on the bodies.
People were gathering at the bank to see if they could find their missing relatives, AFP reported.
“My brother disappeared weeks ago when he was crossing [through] the regime-held zone, and we don’t know where he is or what has become of him,” said Mohammed Abdul Aziz.
Other relatives said their loved ones had gone missing days before. Many had set out for government-held areas, believing that as they were not fighters they would be safe, they said.
Activists say the victims had been killed after being arrested by forces loyal to President Bashar al-Assad.
A Syrian government source said that many of the victims had been kidnapped but accused “terrorists” – the term officials use to describe the rebels – of carrying out the kidnappings and killings.
“They were kidnapped by terrorist groups… and executed last night in a park in Bustan al-Qasr under their control,” the source told AFP.
“Now these terrorist groups are creating a media campaign, showing the bodies being recovered from the Quwaiq river in an area under their control.”
The river’s source is in Turkey, but it flows through both government- and rebel-held territory in Syria.
The district of Bustan al-Qasr has been hotly contested since fighting broke out in Aleppo last July, the BBC’s Jim Muir reports from Beirut.
Aleppo had largely been spared the conflict until that point.