The university reopened on Monday after being closed last month because of protests against a planned increase in tuition fees.
Wits had warned the entire academic year could be cancelled if classes did not resume.
Protesters have been demanding free education.
This is the fourth week of protests sparked by a government proposal to raise tuition fees by up to 8% in 2017.
At least two police helicopters are hovering above the centre of University of Witwatersrand.
It all started out as a peaceful protest of students singing and chanting. They then started disrupting classes and threw stones and bottles at private security guards and police who retaliated with teargas, rubber bullets and stun grenades.
Some students were seen vandalising the university. They are also growing impatient, they say a general assembly meeting which was due to be held last Friday to resolve their issues was cancelled without their knowledge.
The heavy police presence is an indication that both sides are digging their heels in and the situation is unlikely to be resolved anytime soon.
The BBC's Justine Lang in Johannesburg says that a hardcore of 600 out of the 37,000 students at Wit University are "determined not to budge".
President Jacob Zuma ordered a freeze on tuition fees for a year after similar protests last year.
They have been the biggest student protests to hit the country since apartheid ended in 1994.
South African police have fired tear gas at students at Wits University in Johannesburg after they forced their way into lecture halls.