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.
"For now we have removed people with minor to serious injuries, but none critical," she said, adding that firefighters were still searching for commuters who may be trapped inside the train cars.
Radebe earlier said those injured numbered more than 400.
The trains were on the same track, Radebe told The Associated Press, and it appeared that a travelling train collided with a stationery train.
The cause of the accident was unknown and authorities were still gathering information about the collision, 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 Mofokeng.