Officials at Rhodes University, University of Cape Town (UCT) and the University of the Witwatersrand (Wits) announced classes were suspended due to the wave of protests.
Thousands of students have attended rallies focused on hikes in fees that many say will force poor black students further out of the education system.
Protesters at Johannesburg's Wits University blockaded entrances in recent days as students demanded the proposed 10.5 percent fee increase for 2016 was scrapped.
A late-night meeting on Saturday between students and university officials led to a suspension of any decision on the increase while negotiations are held.
The Wits management said in a statement that "the university will officially be closed on Monday" as talks continued.
The universities maintain that the hikes are necessary to provide quality education.
Teaching at UCT, Africa's top-ranked university, also came to a halt, with management describing the disruption of classes by protesting students unlawful.
Students at UCT earlier this year led a high-profile and successful campaign for the removal of a statue of British imperialist Cecil John Rhodes from the campus.
Protests have been held regularly at several South African universities targeting the limited racial transformation of education since the end of apartheid.
Students at Stellenbosch University have been lobbying for more classes to be taught in English rather than Afrikaans, the language of the former apartheid government.
Source: AFP
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