Police said the mother told them she and the children were from Witbank and were left in the field near Zonkizizwe by her husband Tuesday, the South African Broadcasting Corp. said.
Police spokesman Lungelo Dlamini said the cause of the toddlers' deaths will be determined by autopsy. Dlamini said officials suspect the children died of food poisoning.
Earlier this week, the mutilated bodies of two toddlers were found in a store's bathroom in Diepsloot, north of Johannesburg. Three people were in custody and a fourth is being sought.
South African President Jacob Zuma said people who harm children are not welcome in his country and also cautioned against vigilantism.
"These gruesome incidents of extreme torture and murder of our children do not belong in the society that we are continuously striving to build together," Zuma said in a statement released by his office.
"We condemn these murders in the strongest possible terms," he said. "While we appeal to the communities not to take matters into their own hands, we also want to urge them to work with law enforcement authorities to find the perpetrators and prosecute them to the fullest extent of the law."
In third reported incident, the body of a boy, thought to be 4 to 6 years old, was found in a field in Katlehong township, also in Gauteng province, the government statement said. The body also showed evidence of torture and abuse.
Diepsloot residents Tuesday protested, demanding police act quickly to arrest those terrorizing the township, SAFC said.
The bodies of Yonelisa Mali, 2, and her cousin, Zandile Mali, 3, were found Tuesday morning after they were reported missing Saturday, Independent Online reported.
"They were brutally murdered," said Maj. Gen. Oswald Reddy, Honeydew cluster commander. "I can't understand how a human being can do this."
The girls' bodies were found near the home from which 5-year-old Anelise Mkhondo was taken last month. Her body was found a few days later in a trash pile.
No arrest had been made in her death.
"We suspect that it might be a serial killer involved, but it's too early to say," Reddy said.