Russian tricolour flags flew at half-mast as the city observed the first of three days of mourning.
Heightened security measures were imposed in the metro system, which has reopened, but the attack still weighed heavy on commuters.
"Everyone in the metro can only think of this," said 45-year-old Svetlana Golubeva as she entered the Saint Petersburg underground.
Investigators have launched a probe into an "act of terror" but stressed they would look into other possible causes of the blast, which hit a busy central metro line yesterday afternoon.
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Russian authorities have not commented on the alleged bomber's identity.
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 against the jihadists.
Pictures screened on national television showed the door of a train carriage blown out, as bloodied bodies lay strewn on a station platform.
President Vladimir Putin yesterday offered condolences as he was holding meetings outside Saint Petersburg and later placed a bouquet of red flowers at the entrance to one of the stations, Technological Institute, where people have improvised a memorial.
The death toll from the blast stood at 11, with 45 injured, according to anti-terror authorities.
"I will be afraid to take the metro now," said Maria Ilyina, 30, standing near the station. "Before we thought that this would not come to Saint Petersburg - now our city is under threat."
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