Thousands of students have led protests to demand free education for all in South Africa since February in a campaign called 'Fees Must Fall'.
Students across the country have participated in the protests, and clashed with the police. There were reports of protesters throwing rocks at the police, and setting buildings on fire with petrol bombs.
Over 300 people have been arrested during the last six months.
Many universities in South Africa were forced to close down because of the protests, but reopened this week despite ongoing clashes. However, some of the universities, including University of Cape Town would remain closed in the coming days.
University of Witwatersrand in Johannesburg was one of the colleges where students clashed with the police at the campuses.
"The students started throwing sizeable rocks that could have maimed or killed people," the university said in a statement on Facebook.
The police used tear gas shells and stun grenades to bring the crowd under control. Two people were arrested.
The other universities from where protests were reported included University of KwaZulu-Natal in Durban, University of Pretoria, and the University of the Free State.
The University of Cape Town has not given any indication when it will resume its classes.
"The decision allows further time for engagement with key stakeholders, including the Student Representative Council and particularly the SRC candidates who are leading the protest actions on campus at present," the university's spokesman, Elijah Moholola, told Bloomberg. "Private security has been withdrawn from the campus until further notice. Police have not been called onto the campus either."
Media reports say that the cost of university education is prohibitive for many black students, but the universities say that taking away the fee might adversely affect standard of education.
Black students are about four times less likely to attend a university. And even if they do, many drop out because of high tuition rates.
"It's normal for maybe a third to drop out, just because they can't afford it. We paid our fees. But what about those who can't?" said Tshikhudo Milalo, an engineering student from Limpopo province.
The government has promised to cover 2017 fee increases for poor students, and will subsidize education for poor and middle-income families, but the students say that the fee must be abolished altogether.