Meanwhile, police spokesperson Captain Tsekiso Mofokeng told News24 the National Prosecuting Authority and police were working on whether the huge group would get free bail, or whether they would stay behind bars until their appearance in the Brixton Magistrate's Court on Monday.
They were arrested for allegedly violating a court interdict the university had obtained to keep protesters at a distance from campus buildings.
Any other alleged infractions during the protests such as public violence would become clearer on Monday when they appear in court, Mofokeng said.
The EFF said there was no justifiable reason to treat the protesters as criminals, demanding that the university drop charges, and immediately commit to stop outsourcing workers.
"The University of Johannesburg proves its entrapment in the old apartheid idea of dealing with dissent; which is by always unleashing police and security corporal punishment on those who disagree with the authorities," said EFF spokesperson Mbuyiseni Ndlozi, who put the number of arrested at 163.
"UJ must take [a] lesson from other universities where students have demonstrated. The point is to take the moral and logical validity of the protest than to dismiss it with police brutality. No amount of brutality ever manages to suppress the truth: outsourcing must fall."
In the meantime a statement by concerned academics at the university said the interdict was ''excessive'' and not in the spirit of the institution's public function and commitment to free speech.
''The violence and intimidation meted out by security forces is escalating, which is exacerbating and provoking further tension on campus. We call for this to stop immediately,'' said the statement sent by Prof Pier Paolo Frassinelli in the Faculty of Humanities. The statement had been written before Friday's scenes played out, he noted.
A student who was part of a support group outside the police cells in Brixton on Friday night told News24 they had to bring blankets for the huge group because the station only had four.
Mohammed Malek said they were also able to assist in making sure students had any medication they might need because they had prepared for such outcomes at their protests.
He said four ambulances were on standby outside in case there were any medical emergencies.
Mofokeng denied that the holding cells were unprepared for such large numbers, and said anybody arrested has a right to health care and must say if they need their medication.
Former University of Witwatersrand Students Representative Council president and a leader of the #FeesMustFall movement, Shaeera Kalla, was reportedly among those arrested.
While students have gained a first victory in seeing fees frozen for next year, they are also supporting workers who want to be employed directly by the university, instead of being outsourced.
The protests came into sharp focus when students in Cape Town tried to force their way into the National Assembly in the parliamentary precinct on 21 October to speak to Higher Education Minister Blade Nzimande and Minister of Finance Nhlanhla Nene, who was presenting his medium term budget.
Twenty-nine students were arrested during that incident which was marked by the use of stun grenades on protesters.
The protests have spread across the country with students and workers joining forces in a push for free education and the permanent employment of workers, with benefits like medical aid, while universities try to hold crucial end of year exams.
The chairperson of Parliament's portfolio committee on justice Francois Beukman this week said universities needed to refrain from using the police as their frontline in resolving the students' grievances, urging them to rather speak to students and workers first.