The discovery prompted angry protests from residents who looted shops and burned tyres in the street.
Police were holding several people for questioning about the deaths of the girls, who were aged two and three, and were discovered on Tuesday in the Diepsloot area north of Johannesburg after being reported missing at the weekend.
Police are investigating whether they are linked to the death of a five-year-old girl in the same area in September. She had been sexually violated and strangled.
In a separate incident two other children were found dead in Katlehong, east of Johannesburg. Police suspect they were poisoned.
The killings in Diepsloot fuelled angry accusations from residents that police were failing to provide security. Some immigrant-owned shops were attacked, exposing tensions between community members and residents from other African countries.
Nathi Mthethwa, South Africa’s minister of police, urged communities to help police solve crimes such as the killing of the children, saying the government would not tolerate lawlessness in the street.