The authorities suspect the crash was caused by the theft of cables used for signalling, either by people stealing the cables or by striking workers sabotaging the track.
The crash took place at around 7:10 am when a commuter train heading from the western suburbs to the capital ploughed into the back of a stationary train on the same track.
Medical workers said 350 people were treated for injuries by paramedics at the scene.
"Two people are in a critical condition, the driver and one passenger and there are 19 seriously injured," said Mosenngwa Mofi, chief executive officer of railway operator the Passenger Rail Agency of South Africa (Prasa).
It was not immediately known how many children were injured.
"Both of the trains were full of commuters and between them were lots of children on the way to school," said Johan Pieterse of Tshwane Emergency Services. "We counted at least 50 children."
Every day around 20,000 people use the line between Kalafong and central Pretoria.
Rescue workers initially struggled to cut away the tangled wreckage of the trains to free the passengers.
One of the train drivers was freed from the carriage where he was trapped for two hours.
"He's critical at this stage," said Pieterse.
Police and railway investigators zeroed in on the theft of 25 metres of copper cable linked to the signalling system.
The removal of the cable forced drivers to switch to manual operations, which require a control centre to tell drivers if a section of track is clear before they can proceed.
"What caused the accident is still subject to investigation, but cable theft appears to be the cause," said Mofi.
While cable theft is common in South Africa, Mofi speculated that the motive may not have been to get the copper.
He alleged that striking railway workers may have deliberately removed the cable, as part of a pattern of sabotage seen in an industrial dispute with the employers.
"We do have a strong suspicion that it is linked to the current strike," said Mofi. "During the strike there have been serious acts of sabotage," he said.
Transport Minister Ben Martins did not rule out sabotage but said the police and justice department are investigating.
"It is time to see cable theft as an attempted homicide or attempted murder," he said.
The crash is the latest serious rail accident to hit South Africa's ageing urban rail network. In 2011, 857 commuters were injured in Johannesburg's Soweto township when a passenger train smashed into a stationary train during the peak rush-hour period.
Prasa has described its passengers as "travelling like cattle". Over 90% of commuter trains in South Africa are more than 50 years old.
Source: Sapa via I-Net Bridge
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