University of Cape Town youth groups rallied students for Wednesday's protest, which started on campus and snaked toward parliament, about a mile away.
"The group of protesters was massive," said Jabulile Newman, 21, a university junior who attended the demonstrations.
Students stormed parliament grounds, pushing past guards and forcing open the gates. Once inside the grounds, they sat in front of the building to block parliament leaders from getting out.
Police at the scene "started throwing grenades and firing tear gas," Newman said.
Protesters said police used force to try and disperse crowds
"The protest was peaceful but we were met with violence from the police," said Aziz Matthews, 23, a senior at the university.
"We had our hands raised to show we weren't a threat and sat down many times to listen to speeches."
Over a dozen universities in the nation are shut down because of the protests. Students are using the hashtag #FeesMustFall to rally and share experiences on social media.
Protests against fee increases have raged since Monday, with students barricading various entrances to campuses, including UCT and the University of the Witwatersrand in Johannesburg.
Demonstrations escalated Tuesday as students teamed up nationwide to protest the 10% fee hike, which was later decreased to 6%.
"I can speak for a lot of students and say the university fees are exorbitant," Matthews said. "My parents pay my university fees but if they raised it, they would find it very difficult to pay."
In a statement, the South African Police Service said various departments and security forces are helping take "a multidisciplinary approach" to address the protests following Wednesday's incident.
"The behavior of those students is unacceptable and should not be condoned in any way," the South African Police Service said.
It did not address accusations that it used tear gas on students. CNN could not reach the nation's police officials by phone.
The U.S. said it was monitoring the situation in South Africa.
"We've seen the reports (of clashes), obviously concerned by them," said John Kirby, a spokesman for the State Department. "We're looking into it and monitoring it closely. Obviously, our position ... of the right of peaceful protest remains the same."
South African President Jacob Zuma plans to meet with student leaders and university administrators Friday, his spokesman Bonagani Majola said.