Crowds chanted: “Killing of a student, killing of a nation, down with military rule,” at the rare rally in the centre of the heavily-guarded Sudanese capital.
Protesters later blocked a road and set fire to tyres outside Khartoum university. Police fired tear gas canisters and used batons to beat protesters who hurled rocks back at them.
Anti-government-protests erupted at his funeral later on Wednesday.
The government said on Thursday that unnamed armed groups were trying to undermine security at Sudan’s universities – long centres for political activism and debate.
“The government will not allow any disruption to the stability of universities,” President Omar Hassan al-Bashir’s aide, Ibrahim Mahmoud, told the Sudanese Media Centre, an agency which is close to Sudanese security services.
Bashir, who took power in a 1989 coup backed by the army and Islamists, brooks little dissent in Sudan, which has been suffering from an economic crisis since South Sudan seceded in 2011, costing Khartoum more then 70 percent of its oil revenues.
“I remain concerned about a number of human rights issues in the country,” Aristide Nononsi, the United Nations Independent Expert on the Situation of Human Rights in the Sudan, said in a statement on Thursday.
“I continue to hear about cases of arbitrary arrests and detention, as well as allegations of ill-treatment and travel ban on human rights defenders and political activists by security forces.”