Trump expressed his condolences and condemned the attack, which killed 11 people and left dozens wounded. Russian authorities said they were probing an "act of terror."
"President Trump offered the full support of the United States Government in responding to the attack and bringing those responsible to justice," the White House said in a statement about the phone call.
"Both President Trump and President Putin agreed that terrorism must be decisively and quickly defeated."
There was no immediate claim of responsibility for the explosion in Saint Petersburg, which comes after the Islamic State group called for attacks on Russia in retribution for its military intervention in Syria fighting against the jihadists.
Earlier Monday at a White House event, Trump described the attack as "a terrible thing."
Trump's phone call with Putin comes as the US Congress investigates Russian interference in last year's presidential election.
American intelligence alleges that Putin directed a campaign to tip the US election in Trump's favor.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)