The Swedish Transport Administration (Trafikverket) warned commuters to expect lengthy delays to continue after an apparent electrical fault on the line.
As well as the Södertälje to Stockholm line, the failure is also affecting long-distance trains from the capital to Norrköping, Malmö and Gothenburg. They are being redirected through Västerås, meaning that other services will likely experience delays.
"We have staff in place and they are doing all they can," said Roger Falk, press officer for Trafikverket, told the TT news agency.
Replacement buses have been organized but there are still hundreds of passengers left stranded across the capital.
"The buses have been full up and it is hard to find a place during rush hour traffic. It's unfortunate and rather bad luck," added Falk.
The transport agency has urged passengers to get in contact with their train operator and pay attention to any announcements being made at the station where they are based.