Police on Wednesday lobbed teargas shells to disperse AMU students demanding the arrest of protesters who had barged into the campus, shouting slogans over a portrait of Muhammad Ali Jinnah which hangs at the student union office.
District magistrate Chandra Bhushan Singh said two youths were injured in the police action.
Earlier, members of a right-wing organisation had briefly clashed with Aligarh Muslim University students and entered the campus.
They were then taken away to a police station from where they were later "rescued" by other protesters, AMU student union members said.
The protesters were agitated over the portrait of the Pakistan founder which a local BJP MP wanted to be removed.