At least a dozen students from the Walter Sisulu University ended up in hospital after demonstrating at their lack of classroom time because of industrial action by lecturers, who are demanding more money.
Up to 5,000 students who live on campus at the 24,000 student-strong university have been given until midday today to return to their homes while efforts to end the strike continue.
University spokeswoman, Angela Church, said the students had been "extremely patient".
"So we have taken a decision that students must go home."
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Student representative Yanga Socintsa, said the pay dispute between lecturers and university administrators was disrupting their education.
"For the past five weeks there has been no tuition. Our right to education is being violated," said Socintsa.
Lecturers at the financially-struggling public university in Mthatha, in the eastern Cape, are demanding a 10 per cent pay rise.
However, they have only been offered a 4.25 per cent increase. The university, created in 2005, was placed under administration in 2011 after it ran up a 350 million rand (USD 34 million) debt.
The university dispute is just one among several rocking South Africa during the so-called strike season that runs between June and August when annual salary negotiations are conducted.
Tens of thousands of employees in the auto, construction and aviation sectors have downed tools over wages.
Petrol station attendants, motor mechanics and car dealer employees will abandon work next week.
A strike is also looming in the gold mining sector after unions rejected a 6.5 percent offer made by employers on yesterday.