Six people were injured on Sunday as Sudanese police clashed with hundreds of protesters showing support for four dead students originally from the conflict-plagued Darfur region, an AFP reporter said.
Many people were also detained by the security forces, and a bus owned by the city government had been torched, the reporter said.
At least two people suffered head wounds while one was injured in the leg and two women had trouble breathing, apparently from tear gas fired by police, he said.
The death of the four students last week, following an alleged crackdown on a tuition protest, has prompted a re-emergence of Arab Spring-inspired demands for the downfall of the government.
"The people want the fall of the regime," protesters shouted, in a call last heard in Sudan in June and July when scattered anti-regime demonstrations sparked by inflation spread around the country.
They later petered out following a security clampdown.
"Killing students is the killing of the nation!" demonstrators called as they converged on the city's main public bus terminal, the reporter witnessed.
"Peace, justice, freedom!"
About 100 demonstrators walked three kilometres (two miles) from the riverfront University of Khartoum to Nilien University where hundreds more joined them before they moved into the bus terminal.
Police then fired tear gas but the protesters regrouped, and lobbed back stones before more tear gas was fired.
Thick clouds, apparently from the gas, wafted over the western edge of the city as the sun set.
Earlier, about 500 students held a mock funeral at the University of Khartoum for the four Gezira University students, whose deaths a student group blamed on authorities and their "militia."
A student witness said many of the mourners then marched into the street near the campus, where police beat them with batons.
In 1964, the death of student activist Ahmed al-Qureshi sparked the "October Revolution" which ended the military regime then in power after tens of thousands protested.
The Darfur Students Association of Gezira University announced on Saturday that Al Sadiq Yakoub Abdullah and Al Noman Ahmed Gorshi had been found dead along with Mohammed Yunis Neil and Adel Mohammed Ahmed Hammad.
All four had gone missing after joining a peaceful sit-in "for their right to free education in the university," the association said.
"Gezira University administration, the Student Union and National Congress Party militia bear full responsibility for the blood of our martyrs," it said, referring to the ruling party.
Under a 2011 peace deal between the government and an alliance of Darfur rebel splinter factions, the children of people displaced by Darfur's nine-year rebel-government conflict are supposed to get a fee waiver at national universities.
The association said 80 students were arrested and dozens injured when the pro-government Student Union disrupted the sit-in.
Official media announced on Saturday that activities at Gezira University, in El Gezira state south of Khartoum, have been suspended after the students' "drowning."