The crackdown, carried out by state paramilitary troops, appeared to have at least dispersed the sit-in if not cleared it entirely, burning many of its tents and stages in the process. The protesters have been peaceful since occupying the roads outside of the headquarters of Sudan's military two months ago.
Reports from witnesses and live television feeds showed scenes of bloodshed, and the doctors' group said hospitals had taken in hundreds of wounded people.
"The protesters holding a sit-in in front of the army general command are facing a massacre in a treacherous attempt to disperse the protest," the main group organising the protests said. "We call for sweeping civil disobedience to topple the treacherous and killer military council and finalise our revolution."
The TMC, which is led by Lieutenant-General Abdel Fattah al-Burhan, has spent the past weeks visiting the leaders of Egypt, Saudi Arabia and the United Arab Emirates, who have made major financial contributions to shore up Sudan's economy during the transition.
Shams al-Deen al-Kabashi, spokesman for the council, acknowledged the operation in televised remarks but said the military was targeting just one area of the protests, nicknamed "Colombia" by protesters because of prolific drug use that happens there.
Kabashi claimed that clashes at the main sit-in site were a result of protesters from "Colombia" seeking refuge there.
The "Colombia" area is under a bridge spanning the Nile right near the sit-in. Videos posted on social media showed paramilitary troops firing on protesters in numerous spots around Khartoum, from the area around the sit-in to neighbourhoods across the Nile.
Burhan and his deputy, General Mohamed Hamdan Dagalo, commonly referred to by the name Hemedti, were instrumental during Bashir's years in recruiting young Sudanese fighters to reinforce a Saudi and UAE-driven military offensive in Yemen.
Hemedti commands a state security arm called the Rapid Support Forces or RSF that is infamous for its role in an alleged genocide in Sudan's Darfur region over a decade ago. The RSF was widely reported to be the one carrying out the crackdown in Khartoum.
Western governments were quick to condemn the violence, though they offered little in the way of concrete pushback.
"Responsibility falls on the TMC," the US Embassy in Khartoum wrote on Twitter. "The TMC cannot responsibly lead the people of Sudan."
"No excuse for any such attack," wrote Irfan Siddiq, Britain's ambassador. "This. Must. Stop. Now."