The attack on Saturday underscored Kyiv's growing ability to hit deep inside Russia and coming a day after the Russian president refused an offer to meet his Ukrainian counterpart.
St Petersburg governor Alexander Beglov advised the residents not to go outside and warned of possible disruptions to mobile internet service, while regional governor Alexander Drozdenko said 141 drones were shot down over the surrounding Leningrad region.
Russia's defence ministry said its air defences shot down 376 Ukrainian drones.
"Last night, our drones covered a distance of about 1000km to the St Petersburg region - to the enemy navy's arsenals and a base in Kronstadt," Ukrainian President Volodymyr Zelenskiy wrote of the attack on X.
Although no casualties were immediately reported, the renewed attack on St Petersburg is the latest embarrassing blow to Russian President Vladimir Putin's efforts to cast the conflict as a distant event that does not affect Russian daily life.
A Ukrainian drone strike set ablaze an oil terminal in the city and hit a nearby naval base Wednesday, hours before the opening of the St Petersburg International Economic Forum, Putin's annual showcase for investment.
Speaking at the forum, Putin said on Thursday that Russia would strengthen its air defences to counter recent Ukrainian drone attacks, which have reached deep inside his country and cast a cloud over the event in his home town of St Petersburg.
Putin on Friday rejected a proposal by Zelenskiy for a face-to-face meeting on the four-year-old conflict, saying he sees "no point" in it.
Thursday's letter, the first public message Zelenskiy has written directly to Putin since Russia sent troops into Ukraine in 2022, was a sweeping critique of the Russian leader's 26 years in power, as well as some taunts about his age.
Responding to Putin's dismissal of the proposed meeting, Ukrainian Foreign Minister Andrii Sybiha said on Saturday that things would "only get worse for Russia".
"Failures will get more humiliating," he wrote on X, warning that there were "no safe places in Russia that can be exempt" from Ukrainian long-range attacks, and that the intensity of attacks "will continue to grow".
With the front line barely moving as swarms of drones hinder advances, both sides have sought an edge by launching long-range strikes.
In Ukraine, one person was killed and three wounded overnight into Saturday in the Dnipropetrovsk region as Russian forces struck three districts almost 30 times with drones and artillery, regional head Oleksandr Hanzha said.
In Zaporizhzhia, seven people sought medical care after a Russian drone strike started a fire at a parking lot, according to regional head Ivan Fedorov.
Russia targeted Ukraine overnight with 272 strike drones, and air defences shot down 249 of them, the Ukrainian air force said Saturday.
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