Train delays at the Mabopane railway station north of Pretoria on Monday, were due to faulty points near Mountain View, Metrorail said.
The delays caused about 250 commuters to go on the rampage and vandalise the station.
Inspector Paul Ramaloko said the commuters were complaining about trains arriving late and sometimes not at all.
Stones were thrown at trains and at Metrorail offices.
Two ticket office windows and a door were broken and the commuters also attempted to burn down the station.
"Some of the ticket machines and a microwave were stolen," Ramaloko said.
No injuries were reported and no arrests have been made.
He said police were investigating charges of theft and malicious damage to property.
Metrorail spokesperson Thokozani Zitha said an internal board of inquiry will investigate the incident.
"Security measures have been stepped up in that area and currently, the situation is normal although the Mabopane trains are still running behind schedule," he said.
Signal technicians were called out to fix the broken points which took about 40 minutes, he said. - Sapa