Dozens of people were also injured in the explosion which occurred between Sennaya Square and Technology Institute, two busy stations in the centre of the Russian city.
Interfax reported that a bomb was left in a briefcase in a metro carriage and investigators say they are probing a suspected "act of terror".
Anti-terror officials confirmed that a second device was found and deactivated at a station nearby.
Russian news site Fontanka has published a photo of a bearded man dressed in a black hat and coat, who it says is being sought by police over the attack.
The man entered Petrogradskaya station 20 minutes before the blast, it reported.
Search warrants have been issued for two suspects, according to Interfax.
In a statement, St Petersburg governor Georgy Poltavchenko said: "Today, in our city there was a terrible tragedy. As a result of the explosion in the subway people died. Many of the passengers were injured.
"I express my deepest condolences to the bereaved families and relatives.
"Law enforcement authorities and all city services are doing everything necessary.
"In this difficult time we all need to support those who lost their loved ones. I ask all of Petersburgers and guests of our city to be vigilant, attentive and careful."
Earlier, Russian president Vladimir Putin, who is in the city to meet the Belarusian president, expressed his condolences and said terrorism had not been ruled out.
The device deactivated by police was filled with shrapnel, according to an Interfax source.
Russian health minister Veronika Skvortsova said seven people were killed on the spot, another died in an ambulance and two others died at a hospital.
Describing the moments after the explosion, student Maria Smirnova said: "Everything was covered in smoke, there were a lot of firefighters.
"Firefighters shouted at us to run for the exit and everyone ran. Everyone was panicking."
All 62 stations on the St Petersburg Metro were closed after the blast.
Russia's National Anti-Terrorism Committee said security will be tightened at all critical transport facilities.
A UK Foreign Office spokesperson said they were liaising with Russian authorities.
Foreign Secretary Boris Johnson said on Twitter: "Horrified by news of explosion in St Petersburg. My sympathies are with the victims and their families."
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