Nana Radebe, spokeswoman for Johannesburg Emergency Services, said 326 people were rushed to nearby hospitals with minor to serious injuries. No fatalities have been reported.
Firefighters were searching for commuters who may still be stuck inside the train carriages.
The trains were on the same track and it appeared that a travelling train collided with a stationary train.
The accident happened at rush hour between two stations, with both trains travelling from Johannesburg city centre to the township of Soweto, said Lillian Mofokeng, the Metrorail spokeswoman for the Gauteng province.
The cause of the accident was unknown and authorities were still gathering information about the collision, Ms Mofokeng said.
"Our priority right now is just to attend to the injured and then arrange alternative transport," she said. About 100 passengers who were not injured would be bussed home, said Ms Mofokeng.