At Wits, cars were overturned, stoned and hit with sticks along roads near the university as the protests entered a second week.
Rhodes University in Grahamstown was also not left unscathed, with the police firing stun grenades at students protesting against the study fees.
At the troubled Stellenbosch University, the Open Stellenbosch movement occupied the university’s admin building and called for an emergency council meeting because of planned fee increases.
Classes were suspended at most, if not all, of these universities.
As the protests escalated and the #FeesMustFAll campaign gained momentum on Monday, Higher Education Minister Blade Nzimande dismissed statements that the wave of protests constituted a national crisis.
“Yes, it is a challenge, but I would not call it a crisis because we have ways and means to discuss the matter,” he said at a media briefing in Pretoria to address the issue of fee increases at universities.
He, however, conceded that higher education was expensive. “I am very sympathetic to them (students). We are aware that university education is expensive and something needs to be done about it, especially in developing countries.”
He was due to meet university vice-chancellors, council chairpersons and students on Tuesday to find a common approach to the fees saga.
Nzimande said while students were well within their rights to protest and voice their grievances, they should act with restraint.
Following a meeting between President Jacob Zuma and role players in higher education earlier this month, it was decided that a presidential task team was to come up with ways to address the funding problems before the beginning of the 2016 academic year.
Nzimande denied allegations that he had been too quiet about the protests.
“Up to this point, the issue of fees was not a matter of the department. It is a matter of the institutions. It is unfair that I will be the first point of call. I am not the first point of call. When people say I am quiet, I don’t agree with that,” he said.
He also said a promise allegedly made by the government of free education for all was grossly misunderstood.
“Free education is not for everyone. It is for academically deserving poor people…” he added.
Back at Wits, students were outraged after the council failed to show up, citing health and safety reasons.
“If management take a back-door exit, what does that tell you if we’re trying to talk to them?” asked Lesiba Manala, a first-year student.
He said his father’s monthly salary and his mother’s monthly salary together didn’t make the R9 340 for this year’s fees, let alone next year’s.
The students said the planned 10.5 percent increase would exclude those from lower-income families from higher education.
Mcebo Dlamini, the former student representative council (SRC) president, said: “The university doesn’t take us serious. It’s not just today. They have not been taking us serious.” He then led the protesters out of the building.
They took to the street at the Yale Road gate and circled campus counterclockwise till they reached the intersection that leads to the Empire Road exit. Then they sat down.
At nearly rush hour, the traffic on Empire screeched to a halt as the students sang and waited.
Nompendulo Mkatshwa, the president-elect of the SRC, told the group they were there to frustrate the authorities so that city officials would intervene.
An impatient driver had the windscreen of his car smashed after he drove through the seated students.
When police forced the driver from his car, his head was bleeding. While they were putting him in the back of a police car, a few students decided to flip his car. When police pulled their guns, the students retreated.
Wits spokeswoman Shirona Patel said in a statement that the university was still committed to negotiating with student leaders.
She later said the university would be closed on Tuesday.