In the process, police were forced to use tear gas to disperse them. Employees had to be escorted to safety.
The protests hit the Ga-Rankuwa, Soshanguve, Polokwane and Pretoria West main campuses from early in the morning.
The university had to be shut down as students leaders declared they would not allow classes to continue as normal while their peers living off campus were not given any allowances by the university.
Students huddled around the entrance as tyres burnt at the Ga-Rankuwa campus.
They sang Struggle songs.
A student leader said the protest erupted because the university was refusing to give off-campus students meal allowances.
He claimed the vice-chancellor and principal, Professor Lourens van Staden, had been given the powers to resolve the matter, and there had been countless engagements to this effect.
He said despite the involvement of other stakeholders and student leaders, they had repeatedly reached a deadlock.
Another issue the student leader highlighted was the long-standing problem of accommodation.
He said for years the university had battled to provide needy students with accommodation.
“Former minister of higher education and training, Dr Blade Nzimande, noted that the university had a bed shortage of 200 000. We don't understand this as management was given the budget to address this issue.”
Roads leading into the city and to the main campus coming from the R80 highway were blocked by students, with mattresses, rocks and other rubble.
Students also chased away motorists as they made their way through the city centre.
Kingsley Baloyi, chairperson of the EFF Student Command at TUT, said students and their leaders were fed up with university management and the department for giving them the run around on the matters raised.
“We've tried to speak to them countless times and they keep shifting blame between each other. So we've made our way to the department for them to realise that we are serious about this matter and someone needs to intervene.
“We will continue to protest until someone from the department comes to tell us how we are moving forward with this issue.
“And should that fail we will sleep outside the department or the administration block because we brought mattresses along.”
Students lit a tyre on Francis Baard Street, adjacent to the department's entrance, and stopped departmental employees from leaving the premises.
This is the second time this year that the university's academic calendar has been suspended.
TUT spokesperson Willa De Ruyter said classes had been suspended indefinitely across all campuses.