Thousands of students gathered near the Union Buildings, where President Jacob Zuma had been due to address the crowds after he met student leaders and university officials following several days of growing protests.
Protesters tore down sections of a security fence, set fire to portable toilets and hurled bricks at police lines in chaotic scenes.
The Union Buildings are the official seat of the South African government and where Nelson Mandela was inaugurated as president when white-minority apartheid rule fell in 1994.
"But we will keep fighting. South Africa needs to invest more in education. This movement is because we are being oppressed."
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Universities around the country have been closed over the last week as students have protested against the proposed fee rises, which they say will mean poorer black youths are unable to attend university.
The issue of education fees has ignited widespread frustration over a lack of opportunities for young people since the end of apartheid, worsened by a weakening economy and high unemployment.
"I hope that this violent protest ends and that Zuma addresses us with a solution. This movement is by the students, for the students."
Earlier this week, hundreds of students stormed through the gates outside parliament in Cape Town as police struggled to protect the national assembly.
Protests have also erupted daily in Cape Town, Johannesburg, University of Fort Hare in Eastern Cape province and several other provincial cities.
Fees were set to rise up to 10 per cent next year, with a general Bachelor of Arts degree at the University of Cape Town (UCT) currently costing 46,000 rand (USD 3,400).
"The president will use the meeting to gain a first-hand account from students.