Protesters set alight two train carriages and an engine at the Chris Hani station on Wednesday night, Western Cape police spokesman Frederick van Wyk said.
A case of malicious damage to property was opened and no arrests had yet been made.
Regional Metrorail spokeswoman Riana Scott said four carriages, overhead electrical structures, and station facilities were set alight by protesters.
She said Metrorail was forced to suspend train services on the Khayelitsha-Kuyasa-Chris Hani route until further notice. Commuters were asked to use alternative modes of transport on Thursday.
“Police will continue to monitor the situation and Metrorail technical teams will assess the extent of the damage at first light before an estimated date and time for recovery of services can be given,” she said.
The train service from Cape Town to Khayelitsha, as well as all other lines, were operational.