During the protest students danced the "toyi-toyi" - a common display of protest throughout decades of struggle against white rule.
Most South African universities will reopen on Monday despite on-campus clashes between police and students protesters earlier this week, though some, including the University of Cape Town, would remain temporarily shut, media reported.
Demonstrations over the cost of university education, which is prohibitive for many black students, have highlighted frustration at enduring inequalities more than two decades after the end of apartheid.
Nationwide protests erupted last week while universities were on a study recess, with students demanding all universities be shut down until the government provides free education.
The University of the Witwatersrand (Wits) in Johannesburg saw the worst clashes on Tuesday, with students overturning a police car and throwing stones, while police fired tear gas and rubber bullets. During the protest students danced the "toyi-toyi" - a common display of protest throughout decades of struggle against white rule.
Wits said in a statement on Saturday that it would reopen on Monday on several conditions, with students allowed to protest peacefully only in designated areas.
"We are committed to completing the 2016 academic programme and to ensuring that examinations are written," Wits said, adding that it has revised its calendar for 2016.
The academic year in South Africa lasts from February to December.
Other universities set to reopen on Monday after extended recess include Tshwane University of Technology, University of Venda, North West University, University of the Free State and Sol Plaatjie University, according to newspaper City Press.
The University of Cape Town will remain shut down, accoridng to media reports, while the University of Pretoria said in a statement it will conduct a meeting between staff and students on Monday in a bid to resolve the standoff.
The government, grappling with a budget deficit of nearly 4 percent of GDP, has capped 2017 fee increases for next year at 8 percent, but warns that education subsidies should not come at the expense of other sectors like health and housing.