The move follows Lithuania's decision to expel Russian Ambassador Alexey Isakov and the staff of Russia's Consulate General in Klaipeda.
The Russian Foreign Ministry has summoned Virginija Umbrasiene, the interim head of the Lithuanian embassy in Moscow, to inform her about the decision to close the consulate in St Petersburg.
All of the consulate's employees and their families were given 15 days to leave Russia.
The Lithuanian Foreign Ministry said in a statement on Thursday that it regards Moscow’s move as "unjustified and indicative of Russia's continued political and diplomatic self-isolation".
In response to the massacre in the Kyiv suburb of Bucha, the Lithuanian government decided in early April to downgrade the diplomatic representation between Vilnius and Moscow to the level of charges d'affaires and ordered Russia's ambassador to leave the country.
It also decided to close Russia's consulate in the port city of Klaipeda.