The suspect, a native of Armenia and Moscow region resident in his mid-30s, is believed to be "not entirely of sound mind," said city police spokesman Yevgeny Gildeyev.
The man remained in an isolation cell Wednesday at a Kitai-Gorod police station, Gildeyev said, adding that his name would be released at a later date.
Deliberately providing false information about an impending act of terrorism carries a maximum sentence of three years in prison.
Gildeyev said the resulting standoff had Lyubyanskaya Ploshchad blocked off to traffic for around three hours.
At around 9:20 p.m., he said, traffic police on the square stopped a Hyundai Accent for a random document check.
The driver, alone in the car, refused to show his documents and told the officer that he and the car were rigged with explosives.
The man then sped off, only to pull up again next to the FSB building.
Police closed off the area and called a bomb squad to the scene, as well as several ambulances, Gildeyev said.
Television reports showed police officers standing in front of a row of traffic cones and unmarked cars. One picture showed two plainclothes officers -- one in a baseball cap -- apparently talking with the driver of the car.
Police coaxed the man out of the car at around midnight. He was immediately searched and detained. After a thorough search of the car, it was towed away.
Gildeyev said the man was questioned by the FSB and then handed over to police.
"The answers he gave to straightforward questions gave rise to the conclusion that he was not entirely of sound mind," Gildeyev said,
In a meeting chaired by FSB Director Nikolai Patrushev on Wednesday, the National Anti-Terrorism Committee analyzed the way authorities handled the incident, Interfax reported.
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