Police spokesman Colonel Moatshe Ngoepe said a case of culpable homicide was being investigated.
"It is alleged that three people were traveling in a sedan when their vehicle crashed into one of the pipes that was used to barricade the road [by protesters] and went up in flames. Two people burnt to death and one was taken to hospital with serious injuries," Ngoepe said.
He advised motorists to drive with caution in and around Vuwani, especially during the night as obstacles were placed on the roads by protesters. Violence flared up on Tuesday as residents resumed protests against incorporation into a new municipality by the demarcation board.
Cases of malicious damage to property were opened after six vehicles were damaged by stone-throwing protesters.
Some hid in the bush while pelting vehicles with stones, said Ngoepe. The defiant residents, who wanted want Vuwani to remain in Makhado municipality, vowed to shut down the area at a public meeting on Monday.
Last year, as many as 29 schools were either torched or vandalised in Vuwani during demarcation protests.
"The South African Police Service has done maximum deployment in the Vuwani area to protect all the community members and properties during these disruptive actions. The police will continue to monitor the situation until normality returns," Ngoepe said.