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 removed.
AMU spokesman Shafey Kidwai had defended the portrait, apparently hanging at AMU for decades, saying that Jinnah was a founder member of the University Court and granted life membership of the student union.
"Traditionally, photographs of all life members are placed on the walls of the student union," he had told PTI.
The AMU student union today denied media reports that the portrait has been taken down following the controversy triggered by Gautam.
It also said Gautam has been a member of the University Court for three years but has not raised any objections earlier.
Union president Mashkoor Ahmad Usmani told PTI that the Union Hall was being cleaned last evening for an event today in which former Vice President Hamid Ansari was being awarded the life membership.
He said that this may have created the false impression that the photograph had been removed.
Usmani said the AMU union strongly opposed the two-nation theory and the creation of Pakistan, which was a result of the movement led by Jinnah.
"There is no question of being inspired by such a separatist ideology. But we also feel that his photograph is a part of the legacy of undivided India's freedom movement in which AMU played a stellar role", he said.