Thick black smoke could be seen billowing from the station a train was set alight on platform 15.
Metrorail spokesperson Riana Scott said there were some service problems.
Earlier, in a series of notices on Twitter, Metrorail announced delays of about an hour between Salt River and Woodstock on the Southern line, technical problems at Maitland and Woltemade on the Northern line, and technical problems between Ysterplaat and Esplanade.
@TrafficSA tweeted: Cape Town - Commuter Unrest at Cape Town Train Station - Public Order Police arriving
They posted a video in which people were shouting, with banging in the background.