The unrest in Vuwani in Limpopo resulted in the loss of two lives on Tuesday night.
Six other cars were damaged.
Children had not attended school for the second day since the shutdown by protesters.
Two people were killed on Tuesday night when the vehicle they were travelling in burst into flames after hitting a concrete pipe that had been placed as a barricade on one of the roads.
The third person who was in the car is in a serious condition in hospital.
“Whilst all South Africans have the constitutional right to protest‚ as the South African Police Service we reiterate our condemnation of any form of violence and intimidation during protests‚” Phahlane said.
Phahlane said police management had deployed more officers to contain the situation and prevent loss of life.
“We call upon the communities in and around Vuwani to work together with members of the South African Police Service in ensuring the speedy arrests of criminal elements which have engulfed the protest.”
He said the torching of property‚ damaging of vehicles and the loss of life could not be justified as a protest.
Phahlane said these were just criminal activities‚ which must be condemned by all.
“We will not leave any stone unturned and ensure that the perpetrators of this crime are brought to book. Those who continue to blockade roads and damage property will be held liable‚” Phahlane said.
The shutdown‚ which resumed on Tuesday‚ has been organised by the pro-Makhado demarcation task team‚ a community body that is opposed to the inclusion of their areas into the new municipality known as Collins Chabane Local Municipality.