The train cables had since been replaced, the signals were back in order and the trains were running at normal speeds on all lines, spokesman Errol Braithwaite said in a statement.
Earlier on Thursday, delays on the north-south line were caused by around 300 metres of signalling cable being stolen in the Snake Valley area near Pretoria.
The thieves broke through the reserve fence and forced open a locked manhole cover early Thursday morning.
However, train services between Sandton and the airport were not affected.
This was only the second incident of cable theft in the past three years which has caused train delays.
“In 2012 we implemented significantly increased security measures in identified ‘hot spot’ areas. These include rapid-reaction motorbike patrols, dog units and additional guards,” Braithwaite said.
“Since then numerous incidents of attempted theft have been foiled and some arrests have been made. Unfortunately, along with most other utilities, Gautrain does however remain a target.”
Bombela called on the relevant authorities to intensify the battle against cable theft through the Second Hand Goods Act and increased crime intelligence.