When a crowd outside the court heard that charges were withdrawn against the three they began shouting and hurling rubbish bins.
Police fired rubber bullets and teargas to contain the crowd.
One woman was injured.
Earlier, the accused were heard chanting "We will eat you" to the gathering crowd, as they waited inside police vans to be led into the building.
Mbatha walked into the local police station last month and confessed to officers that he was tired of being forced to eat human flesh.
Mbatha named a neighbour with whom he had fought earlier in the day as the alleged mastermind behind the flesh-eating plot.
The news rocked the small town in the KwaZulu-Natal Midlands.
Sukhraj set a bail hearing for October 27.