The measures, taken during the last days of Obama’s presidency, mark a new post-Cold War low in US-Russian ties which have deteriorated over Ukraine and Syria.
Allegations by US intelligence agencies that Russian President Vladimir Putin personally directed efforts to intervene in the US election process by hacking mostly Democrats have made relations even worse.
It was not immediately clear whether President-elect Donald Trump, who has repeatedly praised Putin and nominated people seen as friendly toward Moscow to senior administration posts, would seek to roll back the measures once he takes office on Jan. 20.
The Kremlin, which denounced the sanctions as unlawful and promised "adequate" retaliation, questioned whether Trump approved of the new sanctions. Moscow denies the hacking allegations.
US intelligence agencies say Russia was behind hacks into Democratic Party organizations and operatives ahead of the Nov. 8 presidential election. US intelligence officials also say that the Russian cyber attacks were aimed at helping Trump, a Republican, defeat Democrat Hillary Clinton.
Trump has rejected that conclusion and said on Wednesday that "we ought to get on with our lives," when asked about possible tough sanctions for the cyber attacks.
Should Trump seek to overturn Obama’s measures, he would likely encounter wide bipartisan Congressional opposition.
Obama put sanctions on two Russian intelligence agencies, the GRU and the FSB, four GRU officers and three companies "that provided material support to the GRU’s cyber operations.
Obama said the State Department declared as "persona non grata" 35 Russian intelligence operatives and is closing two Russian compounds in New York and Maryland that were used by Russian personnel for "intelligence-related purposes". The State Department originally said the 35 were diplomats.
A senior US official told Reuters the expulsions would come from the Russian embassy in Washington and consulate in San Francisco. The Russian embassy declined to comment on the expulsions.
The Russians have 72 hours to leave the United States, the official said. Access to the two compounds will be denied to all Russian officials as of noon on Friday, the senior US official added.
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