The State Department said the decision was made "in the spirit of parity," adding that the closures needed to be completed by Saturday.
At the start of Donald Trump's presidency in January, the Republican leader said he hoped for improved relations with Vladimir Putin's Russia.
But after the US Congress approved new economic sanctions against Moscow over its alleged meddling in the 2016 US presidential election, Putin in July ordered drastic cuts in US staff in retaliation.
Along with the San Francisco consulate, the installations ordered closed were a chancery annex in Washington, where Moscow has a giant embassy complex, and a consular annex in New York.
"The United States has fully implemented the decision by the government of the Russian Federation to reduce the size of our mission in Russia," State Department spokeswoman Heather Nauert said in a statement.
"We believe this action was unwarranted and detrimental to the overall relationship between our countries," she added, noting that, with the closures ordered, "both countries will remain with three consulates each."
Putin said 755 diplomatic staff -- both Russian and American -- would have to stop work by Friday, although the US State Department has not confirmed the number.
The number of US diplomatic staff will now be capped at 455, the same number that Russia has in the United States.
"We have waited long enough, hoping that the situation would perhaps change for the better," Putin said when he announced the cuts.
"But it seems that even if the situation is changing, it's not for any time soon."
On Thursday, Washington expressed hope that the two sides "can avoid further retaliatory actions... and move forward to achieve the stated goal of both of our presidents: improved relations between our two countries."
But the State Department warned: "The United States is prepared to take further action as necessary and as warranted."
Washington had already announced it would suspend issuing all non-immigrant visas in Russia between August 23 and September 1.
Visa operations at US consulates will remain suspended indefinitely.
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