Police fired tear gas and stun grenades on Wednesday to disperse students who had stormed the parliamentary complex.
The 29 who appeared in court in Cape Town were not asked to plead.
The protests, sparked by an increase in tuition fees, have forced the closure of South Africa’s top universities.
President Jacob Zuma said he would meet student leaders on Friday to discuss their grievances.
The mainly black students say they cannot afford fee increases.
They have rejected a government offer to cap increases at 6%, down from the 10% to 12% proposed by the management of universities.
Crowds of students gathered outside the court in support of their colleagues.
The 29 have been released from police custody, and the case postponed to February.
Students are marching in the capital, Pretoria, chanting “Union Buildings”, referring to where Mr Zuma and government ministers have their offices, South Africa’s privately owned News24 site reports.
Protests are also taking place in South Africa’s two other main cities, Johannesburg and Cape Town.
Joining in solidarity
The demonstrations began last week at Johannesburg’s prestigious University of the Witwatersrand, before spreading across the country.
Correspondents say the protests show growing disillusionment with the African National Congress (ANC) government, which took power after minority rule ended.
Many black students say they come from poor families, and fee increases will rob them of the opportunity to continue studying.
Financially better-off white students have joined the protest, mainly to show solidarity with the black students.
Mr Zuma’s office said he would meet student leaders and university officials “to discuss the stalemate with regards to university fee increases”.
“It is important that we work together to find solutions. Nobody disagrees with the message that students from poor households are facing financial difficulties and possible exclusion,” he said in a statement.
Correspondents say Mr Zuma’s intervention shows how seriously he is taking the protests.
Students are also demanding the resignation of Higher Education Minister Blade Nzimande, who said on Monday that the protests were not a national crisis.