Authorities shut down the metro system in Russia's second city for several hours as security services said they had also defused a bomb at a second metro station.
Russia's Investigative Committee said it was probing an "act of terror" but added it would look into all other possible causes of the blast.
There was no immediate claim of responsibility for the explosion, which comes after the Islamic State group called for attacks on Russia in retribution for its military intervention in Syria fighting against the jihadists.
Above ground, emergency services vehicles rushed to the scene at the Technological Institute metro station, a key transport hub in the city centre.
As the city prepared to mark three days of mourning, President Vladimir Putin placed a bouquet of red flowers at the entrance to the station in the late evening hours, after chairing a meeting of officials from the FSB intelligence agency, rescuers and the interior ministry.
Anti-terror authorities said in a statement to Russian news agencies that the toll had risen to 11 dead and 45 injured.
"Before we thought that this would not come to Saint Petersburg -- now our city is under threat."
Pensioner Vyacheslav Veselov told AFP he had seen four bodies at the station.
"A station attendant in tears called on the men to help carry the bodies," he said.
The blast occurred in a train carriage as it was travelling between the Technological Institute and Vosstaniya Square stations at 2:40 pm (1140 GMT), said anti-terrorist committee (NAK) spokesman Andrei Przhezdomsky.
The Moscow metro tweeted that it was "taking additional security measures" as required by law in such situations, while NAK said in a statement carried by Russian news agencies that security was being stepped up at transportation hubs and crowded spots across the country.
Putin, who had been in Saint Petersburg holding a meeting at his Strelna presidential palace, offered "condolences" to the wounded and to the loved ones of those killed.
German Chancellor Angela Merkel condemned the explosion as a "barbaric act," while US President Donald Trump spoke with Russian counterpart Vladimir Putin.
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