The Sudanese Professionals Association, which has spearheaded more than four months of protests, said security forces and "remnants of the ousted regime" tried to disperse protesters outside a military facility in the city of Nyala.
Activist Mustafa Baz said clashes erupted when marchers from a refugee camp in Darfur attempted to join the sit-in.The SPA said "many" protesters were wounded.
The attempted break-up comes as protesters have toned down some of their demands in an attempt to ease tensions with the ruling military council that took over the country after ousting al-Bashir last month.
South Darfur governor Maj. Gen. Hashim Mahmoud said around 5,000 people marched form the Otash camp and clashed with troops outside the military facility, according to the state-run SUNA news agency. He said security forces used tear gas to disperse the protesters.
Mahmoud said at least four shoulders were wounded and there were no wounded protesters.