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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.
Pictures screened on national television showed the door of a train carriage blown out, as bloodied bodies lay strewn on a station platform.
Above ground, emergency services vehicles rushed to the scene at the Technological Institute metro station, a key transport hub in the city centre.
Health minister Veronika Skvortsova said the blast had killed seven people on the spot, with three more succumbing to their injuries later.
Thirty nine people were hospitalised, including a 15-year-old girl, Skvortsova said.
"My mom was in the metro, I don't know what's happened to her, I can't get hold of her," one woman, Natalia, told AFP outside the station as she was trying to make a phone call on her mobile.
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.
- 2nd device 'neutralised' -
The blast occurred in a train carriage as it was travelling between the Technological Institute and Vosstaniya Square stations at 2:40pm local time (1140 GMT), said the spokesman of Russia's anti-terrorist committee (NAK) Andrei Przhezdomsky.
The NAK committee later confirmed security services had found another explosive device at the Vosstaniya Square metro station. This device did not explode and it was immediately "neutralised."
The metro network in Saint Petersburg announced it was shutting down entirely after evacuating all passengers.
The Moscow metro also tweeted that it was "taking additional security measures" as required by law in such situations.
NAK said in a statement carried by Russian news agencies that security was being stepped up at transportation hubs and crowded places across the country.
- Putin 'condolence' -
Saint Petersburg announced three days of mourning in the city while President Vladimir Putin, who was holding a meeting nearby in his official Strelna presidential palace, offered "condolences" to those hurt in the blast and to the loved ones of those killed.
Just hours after the blast, people began laying flowers by the Sennaya Square station.
"I was shocked," said local resident Alexander Malikov. "I gathered my friends around and we came to put flowers here."
EU foreign policy chief Federica Mogherini wrote on Twitter she was following developments "together with all EU foreign ministers" gathered for a meeting in Luxembourg.
"Our thoughts are with all the people of Russia," she wrote.
Extremists have targeted Russia's public transportation systems in the past.
In 2013, Russia was hit by twin suicide strikes that claimed 34 lives and raised alarm over security at the Sochi Winter Olympic Games.
A bombing at the main railway station of the southern city of Volgograd killed 18 people while a second strike hit a trolleybus, killing 16.
A suicide raid on Moscow's Domodedovo airport claimed by Islamic insurgents from the North Caucasus killed 37 people in January 2011.
Russia has intervened militarily to bolster Syrian President Bashar al-Assad's forces in September 2015, turning the tables on the battlefield just as rebel forces were strengthening their hold on key areas.
Russian bombardments helped the regime retake rebel areas in the east of the northern city of Aleppo after four years of fighting.
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Pictures screened on national television showed the door of a train carriage blown out, as bloodied bodies lay strewn on a station platform.
Above ground, emergency services vehicles rushed to the scene at the Technological Institute metro station, a key transport hub in the city centre.
Health minister Veronika Skvortsova said the blast had killed seven people on the spot, with three more succumbing to their injuries later.
Thirty nine people were hospitalised, including a 15-year-old girl, Skvortsova said.
"My mom was in the metro, I don't know what's happened to her, I can't get hold of her," one woman, Natalia, told AFP outside the station as she was trying to make a phone call on her mobile.
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.
- 2nd device 'neutralised' -
The blast occurred in a train carriage as it was travelling between the Technological Institute and Vosstaniya Square stations at 2:40pm local time (1140 GMT), said the spokesman of Russia's anti-terrorist committee (NAK) Andrei Przhezdomsky.
The NAK committee later confirmed security services had found another explosive device at the Vosstaniya Square metro station. This device did not explode and it was immediately "neutralised."
The metro network in Saint Petersburg announced it was shutting down entirely after evacuating all passengers.
The Moscow metro also tweeted that it was "taking additional security measures" as required by law in such situations.
NAK said in a statement carried by Russian news agencies that security was being stepped up at transportation hubs and crowded places across the country.
- Putin 'condolence' -
Saint Petersburg announced three days of mourning in the city while President Vladimir Putin, who was holding a meeting nearby in his official Strelna presidential palace, offered "condolences" to those hurt in the blast and to the loved ones of those killed.
Just hours after the blast, people began laying flowers by the Sennaya Square station.
"I was shocked," said local resident Alexander Malikov. "I gathered my friends around and we came to put flowers here."
EU foreign policy chief Federica Mogherini wrote on Twitter she was following developments "together with all EU foreign ministers" gathered for a meeting in Luxembourg.
"Our thoughts are with all the people of Russia," she wrote.
Extremists have targeted Russia's public transportation systems in the past.
In 2013, Russia was hit by twin suicide strikes that claimed 34 lives and raised alarm over security at the Sochi Winter Olympic Games.
A bombing at the main railway station of the southern city of Volgograd killed 18 people while a second strike hit a trolleybus, killing 16.
A suicide raid on Moscow's Domodedovo airport claimed by Islamic insurgents from the North Caucasus killed 37 people in January 2011.
Russia has intervened militarily to bolster Syrian President Bashar al-Assad's forces in September 2015, turning the tables on the battlefield just as rebel forces were strengthening their hold on key areas.
Russian bombardments helped the regime retake rebel areas in the east of the northern city of Aleppo after four years of fighting.
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