Sizwe Kubheka died in hospital last week after the incident left him deaf and with blood clots coming from his nose, according to The Star. The student, aged around 16, lived in Palm Springs, south of Johannesburg.
Before the boy’s death the parents had laid a charge of attempted murder with police, according to the education department.
“The alleged beating happened at school,” said Gauteng province education spokeswoman Phumla Sekhonyane.
“The teacher has been arrested, we have taken him out of the school environment,” she told AFP, adding that the man was later released on bail.
“He is facing a very serious charge, in South Africa corporal punishment is completely outlawed,” she said.
Both the police and education authorities have launched investigations.
The child’s mother told the newspaper that her son returned home complaining of a headache on March 17.
She gave him painkillers because the family could not find transport to hospital, but his condition worsened.
“My boy was deaf just before he died. He couldn’t even hear or see us when we spoke with him at his bedside,” said Maria Kubheka.
“His left eye was swollen and wide open. He couldn’t even blink the eye.
“The last time I saw him, hours before he died, he had blood clots coming out through his mouth and nose.”
South Africa banned corporal punishment in schools in 1996, but as many as half of students still get beaten, according to the Cape Town-based Centre for Justice and Crime Prevention.