The university said it had expelled the first student who was found guilty after an internal disciplinary process two weeks ago.
More than 40 students were arrested in October during several clashes with the public order policing unit.
Students shut down the university, with its north and south campuses turned into scenes of chaos.
The university remained closed for nearly two months.
NMMU spokeswoman Zandile Mbabela could not provide the expelled student's name, saying that due to confidentiality issues, the university could not divulge the students' details.
The university said the student was positively identified in an incident in which cars were stoned outside the north campus administration building in October.
A total of 18 cars were damaged on 20 October on the north and south campuses.
Mbabela said the student was identified by police and campus security, using surveillance footage from the day.
She said 12 more disciplinary proceedings were under way, while seven cases of public violence and damage to infrastructure involving 45 students who were arrested were postponed to later this year.
"There are disciplinary proceedings under way for 12 students in relation to incidents that include disruptions to classes and academic administration processes as well as the arson incidents," Mbabela said.
A student, who asked not to be named as she was implicated, said she had not yet attended a disciplinary hearing.
"I would rather not comment, I don't want to implicate myself any further but it looks as though the university is trying to remove us," she said.
Another student, who also asked not to be named as his case was still under review, said he felt anxious as he waited for the disciplinary committee to make a decision.
"I have made peace with my fate, if I get expelled that's okay," he said.
"I want to finish my studies but if I am forced to leave then so be it. It was all for a good cause."
Another student said he was relieved he would not be expelled after his hearing earlier this month.
"Charges against me were dropped because there was no evidence linking me to the scene," the student said.
"The university does not have evidence. Their identifications are based on witness accounts that do not add up.
"This led to the conclusion that this is a witch hunt and we are just being targeted."
The student was investigated for public violence and damage to infrastructure.
South African Students Congress (Sasco) regional secretary Nobathembu Koko said the organisation was not aware of who the expelled student was and would first have to establish the grounds for the expulsion.
"It would be very incorrect for a student to be expelled for no reason. If #FeesMustFall cases are dealt with nationally, then it is a problem if the university privately expels students," Koko said.
"We are concerned that students have to go to court and await prosecution and then further be prosecuted internally, especially for a campaign that was national."
Koko said, however, that the #FeesMustFall campaign had distanced itself from all criminal acts.
"If this expulsion is regarding those things, we are then speaking of criminals and not students."
Source: Herald
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