In the latest development, many journalists were attacked by group of outraged students, only to be rescued by the police.
In the footage of the unrest, policemen can be seen bringing out journalists from the university campus to save them from the students staging violence.
In the wake of unrest in the university, internet services were suspended in Aligarh district. "There will be no internet services from 2 pm today to 12 midnight tomorrow," district magistrate Chandra Bhushan Singh said.
This has been done to prevent rumour mongering, he said.
It had come to the administration's notice that some anti-social elements could vitiate communal harmony by spreading rumours through videos, using internet services, his order said.
Tension prevailed in Aligarh and students continued with their sit-in at the university's Baab-e-Syed gate, where they had clashed with the police on Wednesday.
They are boycotting classes for the next two days.
The students offered Friday prayers at the scene of the dharna in which a large number of teachers and other members of the AMU fraternity participated.
The controversy began after BJP MP has asked Aligarh Muslim University to explain why it displays a portrait of Muhammad Ali Jinnah, triggering a row days after a student sought permission to hold an RSS shakha on its premises.
In a letter written to Vice Chancellor Tariq Mansoor yesterday, Aligarh MP Satish Gautam objected to the Pakistan founder's picture on the walls of the AMU student union office.
AMU spokesman Shafey Kidwai later defended the portrait, apparently hanging there for decades, saying that Jinnah was a founder member of the University Court and granted life membership of the student union.
AMU vice chancellor Tariq Mansoor today visited the Jawaharlal Nehru Medical College Hospital where three of the students injured in the police lathi-charge are being treated.
The VC later visited the protesting students and assured them of his "solidarity".
AMU Teachers' Association (AMUTA) has sent a memorandum to President Ram Nath Kovind asking him to "urgently institute" a high-level judicial probe into the incident.
They said members of certain outfits entered the campus and disrupted the peaceful academic environment there.
The teachers also plan a peace march up to the district collectorate.
AMUTA secretary Najmul Islam told PTI that they have urged the President to treat the matter seriously as it involved a breach in the security of former Vice President Hamid Ansari.
Ansari was supposed to be felicitated at the University the day the violence broke out.
Islam said protesters who had entered the campus were reportedly carrying firearms.
He said the police, instead of preventing the hooligans from entering the campus, "remained mute spectators".
Watch the footage of the journalist being rescued by the police:
(With PTI inputs)