The driver of the minibus was also killed and seven other children were rushed to hospital, according to officials in Johannesburg’s Gauteng province.
Television images showed that the minibus was destroyed by the fire in the early morning crash in Merafong, more than 70 kilometres (45 miles) west of the city.
Charred schoolbook pages were scattered on the tarmac, as police examined the scene.
“A private scholar transport minibus was involved in a tragic accident in the Kokosi-Wedela area in Merafong, claiming the lives of the 12 learners and their driver,” the Gauteng government said in a statement.
It could not immediately give the ages of the children but said most were from a primary school, where students are normally aged between six and 13.
“They were burnt beyond recognition. When this happens forensics will have to do their part in terms of identification,” Gauteng traffic police department spokesman Sello Maremane told AFP.
Police were investigating what happened but it appeared that the minibus was struck from behind by a small pick-up truck, causing it to overturn and catch fire, authorities said.
The driver of the pick-up was also in hospital, reports said. By late afternoon, most of the children in hospital had been released, reports said.
“I am profoundly saddened by this tragic event,” Gauteng education minister Matome Chiloane said.
South Africa has one of the most developed road networks on the continent but also has one of the worst road safety records, in part due to reckless driving and unroadworthy vehicles.
“I have always said to parents we need to check the condition of the vehicles that we put our kids in,” Chiloane said at the scene of the crash.
Many South African parents have to rely on private minibuses to get their children to school.
“This tragedy, which regretfully is not the first of its kind to confront us, demands that we exercise our obligation to protect our children with the utmost care,” President Cyril Ramaphosa said, offering his condolences.
In the worst road accident in South Africa this year, 45 people heading to a religious event were killed in March when their bus plunged off a bridge into a ravine in the north of the country.
The bus was travelling from neighbouring Botswana to Moria, where an Easter pilgrimage and service have attracted more than a million worshippers in recent years.
In February, at least nine supporters of the African National Congress party were killed in a bus crash as they were travelling home after attending an electoral rally in the east of the country.
And in May, 13 people died in a head-on collision between a minibus taxi and a truck on a major road in the northern province of Limpopo.
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