The portrait was removed from the students' union hall after a BJP parliamentarian sought to know why the institution had displayed it and an outfit founded by Uttar Pradesh chief minister Yogi Adityanath threatened to pull it down.
A student union leader said "some portraits", including that of Jinnah, had been removed for cleaning in view of a programme to felicitate former Vice-President Hamid Ansari. Sources, however, said none of the other portraits of honorary lifetime members of the students' union, including that of Mahatma Gandhi, had been brought down.
Ansari's event was called off on Wednesday evening and he returned to Delhi.
Six persons were injured in police action after students were locked in a face-off with suspected activists of the Hindu Yuva Vahini, founded by Adityanath, when they tried to barge into the varsity.
Divisions have emerged within the BJP itself over Jinnah, laudatory comments about whom had cost L.K. Advani dear over a decade ago.
An Uttar Pradesh minister was quoted as saying on Tuesday that Jinnah was a great man and the protesters should "stop questioning the AMU over his portrait". The minister denied the statement after an MP called for his ouster.