The blast occurred around 2.30 in the afternoon as the train was traveling in a tunnel from Sennaya Ploshchad to Tekhnologichesky Institut station in the city.
Tekhnologichesky Institut is a cross-platform interchange station of the Saint Petersburg Metro.
Following the attack, city's metro system has been shutdown.
Bodies were seen strewn across the station platform outside the train, while rescuers carried injured victims out of the station.
The Anti-Terrorism Committee said no outfit has claimed responsibility for the attack so far.
A spokesman for the National Anti-Terrorism Committee said the blast was caused by an unidentified explosive device in one of the train's cars.