St Petersburg governor Alexander Beglov said the city of six million had come under a "large-scale" drone attack, with the city's oil terminal struck.
He said there were no casualties and the aftermath of the attack had been dealt with.
Ukrainian President Volodymyr Zelenskiy confirmed the strikes and said a military facility had also been hit.
"Ukraine's defence forces struck port oil infrastructure that generates revenue for Russia's war, and also hit Kronstadt, an important military target more than 850 km from Ukraine's state border," he said on Saturday.
Leningrad region governor Alexander Drozdenko said drones had struck the port of Vysotsk, about 170 kilometres northwest of St Petersburg on the Gulf of Finland. The port handles oil, grain, coal and liquefied natural gas.
Drozdenko said 72 drones had been shot down over the Leningrad region.
Ukraine has intensified strikes on Russian energy infrastructure in 2026, causing fuel shortages in parts of Russia.
St Petersburg, about 900km from Ukrainian-held territory, has occasionally come under attack from Kyiv's drones.
Targets have included the city's oil terminal and a moored warship during the St Petersburg International Economic Forum in June.
South of St Petersburg, the governor of Pskov region said more than 30 drones had been shot down overnight. He reported minor damage and injuries, including to a factory in the town of Velikiye Luki.
Late on Friday, a massive Russian glide bomb strike on the northern Ukrainian city of Sumy killed at least four people, including a child, and injured 27, according to its regional governor.
Other areas in Sumy region and in southeast Ukraine closer to the front lines also came under Russian attack, killing a total of six people.
"At the epicentre of the strike - a high-rise apartment building, a shop and a street," Oleh Hryhorov wrote on Telegram of the strike in Sumy.
Hryhorov said the dead included a five-year-old child and her mother. The injured were being treated in hospitals, he said, including a 13-year-old in serious condition.
To the southeast, more than 50 strikes involving drones, artillery and bombs killed three in Dnipropetrovsk region, including two near Nikopol, a town on the opposite bank of the Dnipro River from the Russian-held Zaporizhzhia nuclear power plant.
Twelve people were injured, regional governor Oleksandr Hanzha said on Telegram.
Two people were killed in a strike in the city of Zaporizhzhia, a frequent recent target of deadly attacks, regional governor Ivan Fedorov said.
A total of 21 people were hurt. Fedorov said new attacks were launched on the city late in the evening.
The capital Kyiv was observing a day of mourning, a day after a Russian missile and drone attack killed at least 30 people in the deadliest strike on the city in 2026.
Meanwhile Russia's military says its forces have taken control of Kostiantynivka in eastern Ukraine, a key locality whose capture Moscow has long sought in its advance through the Donetsk region.
General Valery Gerasimov, in a report to Vladimir Putin on the conduct of the war, now in its fifth year, said the southern group of Russia's forces was "carrying out offensive operations to liberate" all of Donetsk Region.
The Defence Ministry's post on the Telegram messaging app showed what it said were scenes from the captured town, including pictures of Russian servicemen holding up national flags around shattered buildings.
Ukraine's general staff denied Kostiantynivka had fallen.
"We deny this. These are more fake claims," a general staff official said.
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