Wits University in Johannesburg, where the protests began, the University of Cape Town and the University of Western Cape remain closed.
The BBC's Pumza Fihlani in Johannesburg reports that students say a number of their other demands have been overlooked. These include racism at the country's previously white institutions and free education for the poor.
The students are also demanding that exams, which they are due to take this week, be postponed indefinitely.
Analysis: Pumza Fihlani, BBC News, Johannesburg
The government had expected an end to protests after President Jacob Zuma agreed to a 0% increase on tuition fees.
But the continued protests should not come as a surprise. During the nationwide demonstrations, it became clear that the protests were not just about fees but also often unaddressed challenges in South Africa, including racial inequality.
Many here say they are still feeling the effects of apartheid, despite its collapse more than 20 years ago, and feel the government is failing to rectifying this.
"Our parents were made promises in 1994. We're just here for the refund" reads one of their most popular placards.
And it seems this group want all or nothing.
Education is one area where students say it is most evident that the playing field is not level between black and white people.
They want the government to honour the promises it made when it took power in 1994, one of which was free education for all. They believe this will help them out break the cycle of poverty and unemployment.
Last week police used stun grenades and water cannon to stop a group of students breaking into government buildings in Pretoria.
Universities had said they needed to increase fees to maintain standards, and that they had been hit by a reduction in government subsidies.
President Jacob Zuma agreed to provide more government money for universities in a private meeting with student representatives and university management on Friday.
In that meeting the government said it did not know how much they would pay or where the money would come from, one of the attendees Vice-Chancellor of the University of Cape Town, Max Price, told the BBC.
Mr Zuma then announced on TV that the fee increased would be frozen.
But some students continued protesting, angry that Mr Zuma spoke on TV, rather than speaking to the crowds directly.
On Sunday, Wits students resolved to carry on protesting.