The CCMA recommended an 8% increase, however, SANParks said it could only afford 6.5%.
The disruption meant students could not get food in campus cafeterias and had to be given vouchers.
The police and Tshwane Metro Police Department have deployed more officers to the CBD to ensure that calm is restored.
Lieutenant General Elias Mawela said the police would look into all allegations and assured the taxi industry that feedback would be given shortly.
The cows belonged to neighbouring villagers and had been herded onto the campus.