Police forces entered the Azhar University campus in response to a university administration request after escalating violence left one student dead on Saturday, the Egyptian state television reported.
The police arrested 100 students suspected in taking part in acts of violence, it said.
According to the state television, "terrorist students" set the faculty of agriculture alight.
Video footage showed smoke rising from the faculty of commerce building.
The university has postponed some commerce faculty exams but will proceed with the rest of the exam schedule as planned.
The Azhar University has been witnessing protests against what the Muslim Brotherhood calls a military coup that toppled former Islamist President Mohamed Mursi.