Russian staff had left the consulate last month, after Washington ordered Moscow to vacate some of its diplomatic properties, part of a series of tit-for-tat actions during a thorny phase in bilateral relations.
Since then, US officials had occupied administrative parts of the compound but on Monday they entered residential areas that the departing staff had locked, the ministry said in a statement late on Monday.
"Despite our warnings, the US authorities did not listen to reason and did not give up their illegal intentions," it said. "We reserve the right to respond. The principle of reciprocity has always been and remains the cornerstone of diplomacy."
Footage aired repeatedly on Russian state television showed what the broadcaster said were US officials breaking locks that had sealed off parts of the compound and entering the buildings.
The "intruders" had taken over the whole premises including the consul general's residence, the ministry said.
"Therefore, we understand that Americans, breaking into our diplomatic buildings, have de facto agreed that their missions in Russia may be treated likewise."
"Electoral interference"
In San Francisco, a Department of State Diplomatic Security guard answered the door at the Russian consulate, a six-storey brick building surrounded by a modest security fence and manicured hedges in the Pacific Heights neighborhood. The guard declined to comment and left the building in a black SUV.
A sign on the front door said that the consulate was closed and gave a new mailing address. The State Department guard left the consulate front door open, behind a closed gate, and sounds of activity could be heard inside, but no one responded to repeated calls by a reporter.
Russian President Vladimir Putin last month accused Washington of "boorish" treatment of Russia’s diplomatic premises on US soil, ordering the foreign ministry to take legal action over alleged violations of Russia’s property rights.
The dispute began late last year when former US president Barack Obama expelled 35 Russian diplomats on accusations of Russian meddling in the election that took Donald Trump to the White House.
Trump took office in January, saying he wanted to improve ties with Russia, while Putin also spoke favourably of Trump.
But the allegations of interference in the vote, which Moscow has denied, have persisted as an investigation by US authorities has widened.
In July, Moscow ordered the United States to cut the number of its diplomatic and technical staff working in Russia by around 60 percent, to 455.