Goals from Paddy Madden, Ed Upson and Dan Burn condemned the Bees to only their second league defeat in 16 matches - and maintained the Glovers' play-off hopes.
The visitors, who are looking ahead to an FA Cup replay at Stamford Bridge this month, dominated the early periods with Clayton Donaldson and Tom Adeyemi both twice thwarted by goalkeeper Marek Stech.
Yeovil broke the deadlock against the run of play on 34 minutes when Tony Craig's attempted clearance hit Kevin Dawson, falling perfectly into the path of the onrushing Madden to notch his seventh goal in four games.
Then, just before the break, midfielder Upson lit up Huish Park on his 100th appearance for the Somerset side with a rasping 25-yard thunderbolt which flew into the top corner of the net.
In the second period, James Hayter and Luke Ayling both came close to adding a third - before Burn volleyed home.
Brentford last week