Pontus Jansson's last-minute header broke Watford hearts and gave Brentford a third successive Premier League win for the first time.
It looked like Emmanuel Dennis' powerful strike after the break had secured a point for Watford, but the result pushes them even closer to an immediate return to the Championship.
Christian Norgaard had put the Bees ahead inside 15 minutes.
It was a game of small margins as moments before Jansson's strike, Imran Louza had missed a chance to win with the goal gaping.
The result leaves Watford in 19th, six points adrift of safety having played two more games than Everton.
Brentford took the lead through Norgaard; Kristoffer Ajer flicked on Ethan Pinnock's long throw, and the Dane was there to apply the close-range finish.
There was a stagnant feel to the game for much of the first half. Ismaila Sarr and Dennis were trying to combine and restore parity for Watford, but they struggled to impose themselves.
But the tide turned in the first 10 minutes of the second half. At one end, Ivan Toney squandered a chance to double Brentford's lead, before Dennis fired home from a tight angle to make it 1-1.
Initially disallowed for offside after Sarr's flick on from Moussa Sissoko's cross, VAR intervened and the goal counted to give Vicarage Road an entirely new impetus.
The home side pushed for a crucial winner, and after hitting the bar with a free-kick through Dennis, Louza somehow failed to score from an open goal before Jansson provided the Bees' sting in the tail.
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