The police, backed by the paramilitary Rapid Support Forces, moved against the angry demonstrators after dozens of protesters blocked Nile Street, a major avenue in the city, for the second consecutive day. Protesters also blocked a road leading to the capital's northern district of Bahari.
The forces dispersed about 100 protesters, but there were no reports of casualties, Presstv Reported.
A witness told Reuters forces dismantled barriers that were erected by protesters at the entrance to a key bridge, causing traffic jams. Traffic in the capital had come to a near standstill.
The dispersal came as stalled talks between the opposition and the TMC resumed on Monday over handing power to a civilian administration after a deadlock in negotiations.
The meeting was being held behind closed doors at a convention centre in central Khartoum.
The much-awaited discussions came with crowds of protesters still camped round-the-clock outside the army headquarters in central Khartoum.
Taha Osman, a spokesman for the protest movement said late on Monday that an agreement had been reached with the country's military rulers on the makeup of a new "sovereign council" to run the country. "At today's meeting we agreed on the structure of the sovereign council which will include military and civilian representatives."
The Sudanese Professionals' Association, which spearheaded demonstrations, and some other factions have been locked in negotiations with the TMC over a proposed joint civilian-military body to oversee the country.
The military generals and protesters are at loggerheads over who will sit on a new ruling body that would replace the existing military council. The generals have proposed that the new council be military led, while the protest leaders want a majority civilian body.