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In a written ruling, Ofcom said the phrase could offend homosexuals and should not have been used.
Clarkson used the phrase during a discussion with the studio audience about the rounded, two-seater Daihatsu Copen.
An audience member described the car as "gay" and Clarkson replied: "A bit gay, yes - very ginger beer".
The watchdog said "gay" can be used to mean "foolish, stupid and socially inappropriate, or disapproved of and lame".
But Clarkson's response made it clear he was using the word to refer to homosexual people, Ofcom said.
"This ... meant that the use of the word became capable of giving offence," Ofcom said. "In the context, there was no justification for using the word in this way."
Five viewers complained about the show, broadcast last July on BBC Two.
Ofcom said the BBC had reminded producers and presenters to avoid using derogatory comments about sexual orientation and the matter was resolved.
