The closure of the British Council's Moscow office will sever cultural ties, while that of the consulate general in St. Petersburg will end Britain's diplomatic presence in Russia's second city.
The Kremlin has warned that Russian Federation could take further measures, if Britain makes any more "unfriendly" moves toward Russian Federation.
The move followed Britain's decision on Thursday to expel 23 Russian diplomats over the attack in the English city of Salisbury which left former Russian spy Sergei Skripal, 66, and his daughter Yulia Skripal, 33, critically ill in hospital. They remain in critical condition and a policeman who visited their home is in serious condition.
The announcement is the latest development in an ongoing worldwide saga that began on March 4, when Sergei Skripal, a former Soviet and Russian spy, was found unconscious on a bench next to his daughter, Yulia, in the English city of Salisbury.
As the dispute between Britain and Russia mounted Saturday over the poisoning on British soil of a former Russian spy, with the Kremlin announcing the expulsion of 23 British diplomats, Russia's foreign ministry came up with yet another theory about the origin of the toxin used.
The British Council said it was profoundly disappointed by Russia's decision and remained committed to developing long-term people-to-people links with Russian Federation despite the closure.
The Russian Foreign Ministry said the 23 British diplomats had one week to leave the country.
Western powers see the nerve-agent attack as the latest sign of alleged Russian meddling overseas.
"These will then be despatched to highly-reputable global laboratories selected by the OPCW for testing with results expected to take a minimum of two weeks", said a Foreign Office statement.
The row comes as Russian Federation heads to the polls in the country's presidential election.
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The Russian foreign ministry said the United Kingdom staff would be expelled from Moscow within a week in response to Britain's decision to expel 23 Russian diplomats.
Speaking to Robert Peston on ITV, McDonnell also defended Jeremy Corbyn's apparent reluctance to avoid blaming the Russian state or Putin for the poisonings, insisting that it was right that the leader of the opposition held the government to account.
Associated Press writer Angela Charlton in Moscow contributed.
On Friday, Russia said it could hit back at Britain at "any minute" with its own raft of punitive measures. Topping the list was Britain itself - the other three, Slovakia, the Czech Republic and Sweden.
The diplomatic row has now led to calls for tough action against Russian Federation and for the country to be stripped of this summer's football World Cup.
Czech Foreign Minister Martin Stropnicky rebuffed Zakharova's assessment, saying, "We reject such groundless statement on the origins of the Novichok". It is still not clear how the Skripals came in contact with the nerve agent.
Authorities were also appealing to patriotic feelings by holding the vote on the anniversary of Russia's 2014 annexation of Crimea from Ukraine.
Russian Federation also suspects foul play in Glushkov's death and opened its own inquiry Friday.
And Washington slapped sanctions on Moscow over alleged election meddling.Since first being elected president in 2000, Putin has stamped his total authority on Russian Federation muzzling opposition and reasserting Moscow's posture abroad.He has sought to use the campaign to emphasise Russia's role as a major world power, boasting of its "invincible" new nuclear weapons in a major pre-election speech.
Lawless contributed from London.