A Pretoria police officer, who asked not to be named, told Times Live: "At the moment it appears that two people are dead, with a heck of a lot more badly injured".
Mofokeng said more than 300 people have sustained minor injuries.
"For now, I can confirm that we have closed the Mabopane line until the scene has been cleared and investigations have been concluded", said Metrorail spokesperson Lillian Mofokeng.
Rescue workers are carrying passengers out of the train wreck.
In 2016-17, 495 people were killed on the country's railways according to the Railway Safety Regulator - an increase of eight per cent on the previous year.
The scene of the accident was said to be chaotic and people were advised to avoid the area.
"If it's found that there's been negligence, a charge of culpable homicide might be opened", Masha said.
"We are deeply shocked by this tragic accident so early in the new year".
It has been reported the two trains crashed head-on into each other, causing both to derail.
Fifty ambulances were at the scene and three helicopters assisted with getting critically injured patients to hospitals. But I think there's a need now to immediately have a meeting with Prasa (Passenger Rail Agency of South Africa).
The city's mayor, Solly Msimanga, sent his condolences to the victims' families via his official Twitter account.