Police at the Fort Hare campus used water cannon to force back students who tried to march on the venue where dignitaries including President Jacob Zuma and Mugabe were gathered.
The students later staged a protest vigil after their bid to block the main entrance was thwarted by police.
"Students tried to barricade the roads leading to the university," police spokesman Khaya Tonjeni told AFP.
"We have reinforced the security because there was a high level of intimidation two days ago when marquees were burnt down," he said.
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The violence at Fort Hare follows protests at campuses across South Africa over the past year by students over issues such as racism, fees and accommodation.
Several universities were closed briefly in February after a wave of protests in which buildings were torched, while an auditorium was firebombed at the University of Johannesburg earlier this week.
"Burning schools, libraries and university buildings means burning the future," Zuma said in his address at Fort Hare.
"There can be no justification of violence and anarchy, especially in a country where people have freedom of speech and expression."
Mandela said in his autobiography that Fort Hare was like "Oxford and Cambridge, Harvard and Yale, all rolled into one."
Mugabe today lauded the university where "I was transformed and... Truly discovered my African identity and African personality."
Mugabe, 92, repeated his vow that he would not step down despite ruling since 1980.
"In Zimbabwe they have said we will have regime change, I have said never ever, and that's one of the reasons I have stuck on," he said.