Another 300 people were hurt, with 82 sustaining serious injuries.
"The current fatalities stand at three, but it still might rise," said Mabaso.
When paramedics arrived on the scene, they found carriages from both trains tilting half off the track.
"Numerous passengers were found either in the trains or found walking around on the scene," Russel Meiring, a spokesman for the ER24 emergency services, said in a statement.
Rail accidents are common in South Africa.
A year ago, in one of the country's worst rail disasters, a passenger train travelling from the southern city of Port Elizabeth to Johannesburg smashed into a lorry at a level crossing near Kroonstad in the central Free State province and burst into flames, killing 19 people and wounding 254.
In 2016-17, 495 people were killed on the country's railways according to the Railway Safety Regulator -- an increase of eight percent on the previous year.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)