The demonstrators chanted "civilian, civilian" as they gathered in front of the National Ribat University in Burri neighborhood near the ministry of defense, but security forces quickly chased them and beat them with batons, a Reuters witness said.
A few protests have taken place at night in Khartoum and other state capitals since security forces stormed a sit-in outside the Defence Ministry on June 3, killing dozens. But Monday's was the first demonstration in Khartoum to be held during the day.
Talks between the military and an opposition alliance collapsed after the sit-in was dispersed.
The sides had been wrangling for weeks over whether civilians or the military would control a new sovereign council to lead Sudan to elections after the military deposed and detained long-time president Bashir on April 11.
Ethiopian Prime Minister Abiy Ahmed and the African Union (AU) have been trying to mediate between the sides.
The council on Sunday rejected Ethiopia's proposal which the opposition coalition agreed to on Saturday, but did agree in principle to the AU's plan.
The Sudanese Professionals’ Association, the country's main protest group, said in a news conference on Monday that the military council is "systematically trying to undermine the gains of the revolution by destroying freedom of expression and violently dispersing the protests they call for."
The group also said it will continue escalating protests and that it is organizing a big demonstration on June 30.
The prolonged chaos has concerned world powers including the United States, which sanctioned Sudan under Bashir over its alleged support for militant groups and the civil war in Darfur.
The opposition accused the military council of ordering the sit-in's bloody dispersal and wants an international inquiry. Witnesses said the paramilitary Rapid Support Forces, headed by the military council's deputy, carried out the violence.The military said a crackdown on criminals spilled over to the sit-in area, but some officers have been detained for presumed responsibility.