The move comes one day before Moscow's deadline for US personnel to leave their positions and will take effect Saturday.
"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 announcing the decision. "We believe this action was unwarranted and detrimental to the overall relationship between our countries."
"In the spirit of parity invoked by the Russians," she continued, "we are requiring the Russian government to close its Consulate General in San Francisco, a chancery annex in Washington, DC, and a consular annex in New York City."
Nauert also noted the United States was allowing Russia to maintain additional annexes "in an effort to arrest the downward spiral in our relationship," but was "prepared to take further action as necessary and as warranted."
White House press secretary Sarah Huckabee Sanders told reporters that the decision to close the Russian diplomatic facilities was made directly by Trump.
"This was a decision made by the President," she said.
The Russian Foreign Ministry acknowledged the move in a statement on their website, saying Tillerson spoke directly with Russian Foreign Minister Lavrov in a phone call, and that Lavrov "expressed regret at the escalation of tension in bilateral relations, which was not initiated by (Russia), and indicated that Moscow will carefully study the new measures announced by the Americans, after which we will inform them of our reaction."
Back in Washington, a senior administration official told reporters on a conference call that the United States would not be expelling any Russian personnel through this action, and that the Russian government could reassign its staff to other consulates or annexes. The two affected annexes, the official said, housed Russian trade missions.
Despite the order, the official insisted the administration's goal "is really to find a way to get to better relations between our two countries."
The Russian Consulate in San Francisco issued a statement
responding to the decision on Facebook and Twitter stating: "We believe that the decision to close the Consulate General of Russian Federation in San Francisco is another unfriendly step of the US authorities."
The move is the latest in a series of escalating diplomatic penalties between the United States and Russia that began in the aftermath of last year's US presidential election.
In July, the Russian Foreign Ministry ordered the United States cut its diplomatic staff in Russia by nearly half and announced it would seize
two US diplomatic properties in response to expanded sanctions passed by Congress.
The senior administration official who briefed reporters Thursday confirmed that the United States has fully complied with Russia's staff reduction order, and that visa processing -- which was temporarily halted after the initial announcement -- will resume shortly at a "much-reduced rate."
In late 2016, former President Barack Obama ordered the expulsion
of 35 Russian diplomats, and the seizure of two Russian government compounds in response to alleged Russian meddling in the US presidential election. At the time, the Kremlin announced it would not retaliate immediately, but rather, consider further action "based on the policies of the Trump administration."
Clarification: A headline on a mobile alert that accompanied this story said Russian officials are being "tossed." While the diplomatic facilities are being closed, a senior administration official says the US is not expelling any diplomats and those individuals can be reassigned by Russia.