Ten students from the Fort Hare University's Alice campus have been arrested and will be charged with public violence and other related charges.
Student leaders threatened to march to the local police station in their thousands but police believe that the situation is now under control.
Academic activities had to be suspended on Wednesday after students blocked the entrance to the university, pelted cars with stones and even looted a local business truck.
Police spokesperson Brigadier Tembinkosi Kinana says there is a strong police presence on campus and the situation will be closely monitored.
The University said in a statement, in an effort to restore calm and stability, the Registrar invoked an existing court interdict which prevents students from disrupting campus operations. The Registrar gave the students advance warning that the court order would become effective and that by law police will have a duty to restore peace.
In January. 14 students were arrested when violence broke out on both the Alice and East London campuses.
The 11 students arrested in East London were released following their first court appearance due to a lack of evidence to prosecute them.