Details of the unrest at Wits University on Tuesday were widely shared on social media. Some protesters threw rocks as police and private security guards tried to clear the scene.
However, Twitter users -- using the hashtag #feesmustfall -- said that some students also offered flowers to the police, and shouted "we want peace."
Student leader Mcebo Dlamini condemned "police brutality" but was later arrested, according to reports from witnesses at the scene.
The fees issue sparked previous violent protests in South Africa last year, when demonstrators barricaded universities and stormed the South African Parliament to press their message that university education in the country is too expensive, among other issues.
President Jacob Zuma later announced that universities would not increase fees in 2016 as planned. Students celebrated, but many posting on social media said fees remained too high and worried about what would happen after 2016.
Last month, a fresh wave of protests and unrest broke out at universities across South Africa after the government announced fees will rise next year, with an 8% cap. This university has been shut down for the past two weeks.
It reopened this week, but the senior executive team at the university said in a statement issued Tuesday that a group of students wearing balaclavas had refused to disperse at the main campus in Braamfontein and there had been an attempt to disrupt lectures.
"We have reports of two students being arrested and one student and one staff member being injured," a further statement added.
They advised staff and students not involved in the protest to stay indoors and lock the doors.
Major General Vuyisile Ngesi, a spokesman for the South African Police Service, told CNN Tuesday: "At the moment we cannot determine the exact number of protestors but it was a considerably huge number of the student population involved.
"Police used tear gas, rubber bullets as well as stun grenades to disperse the protesters in order to prevent them from taking the protest action to the streets closest to the university."
"The situation is calm now on campus but the police are present and monitoring the situation," added Ngesi.
There were reports of unrest at other universities this week too. The hashtag #UCTshutdown was widely shared on Twitter, relating to the University of Cape Town.
One Twitter user, Nigel Patel, posted a picture Monday of what appeared to be majority white students, commenting: "These are the kids you are opening UCT for."
Patel told CNN the picture was taken in a law lecture on the UCT campus, adding: "I don't want to comment too much on the picture, but found that it is a strong statement on the privilege and divide that exists at UCT."
Amid the protests, students at a number of universities have said they want to return to lectures.
According to Professor Adam Habib, Vice-Chancellor and Principal of Wits University, 77% of students polled wanted to return to class.
"Our job is to protect the rights of everyone, including the students and staff who want to learn and work," he said.
"The protestors acknowledge that access to quality higher education for the poor and what is referred to as the missing middle is a national problem that cannot be resolved by any single institution."