In his defense, the university said that Mphahlele had threatened to interrupt the graduation ceremony, harming people and property.
"Closer to the day of the graduation ceremony, the threat of disruption has escalated the threat of violence, damage to people and property," said senior communications manager Lebogang Seale.
"In its assessment, the university has decided to apply strict access control to the campus and to the graduation site to ensure that all people and property in our facilities are safe and secure."
Seale said that it was clear that Mphahlele had no intention of attending the university's call for him to cooperate, since he had started a demonstration inside the venue.
"It's unfortunate that anyone wants to take any actions that seek to infringe the rights of other students and staff … The university has several avenues for students to raise any complaints they may have," the university said.
It was not the first time a graduation ceremony was interrupted at the institution this year.
In early April, a bachelors in arts rose to the podium, but refused to be conferred with his diploma. He accused the institution of racism. It was removed from the premises by security.