Lasse Vibe netted a first-half double for the Bees which followed a Nico Yennaris close-range finish to make the result all but secure by half-time.
Zach Clough scored a second-half consolation from the penalty spot for the Trotters after Alan McCormack was penalised for a foul.
Bolton are 17 points from safety with six games remaining in the season.
Defeat for Bolton extended their dreadful sequence of no away wins in a year and means defeat at Derby at the weekend will spell relegation for Wanderers.
A second win in as many games for Brentford lifted them 12 points clear of the bottom three.
Alan Judge was the creator of the home side's first chance when he almost looped a cross from the right over Ben Amos, but struck the bar.
The midfielder provided a pinpoint cross from Vibe's second goal with a header, which was the Denmark striker's third goal in two games.
Brentford manager Dean Smith:
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"If you'd said to me three weeks ago that we'd have two wins on the spin at Nottingham Forest and again here, I'd have bitten your hand off.
"It means we can go to Ipswich on Saturday and try to make it three wins in a row and then we can be looking at a top 10 finish.
"I wanted more goals but with the run of form we've been on I wanted a result and that was the most important thing."
Bolton caretaker manager Jimmy Phillips:
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"We have to give the supporters something to cheer about rather than give them the kind of displays we gave in the first half tonight.
"In the second half we were more competitive and we always say we have to compete before we can play.
"Before the break we were nowhere near as competitive as we needed to be."
Bolton could be relegated to League One on Saturday after they were beaten by Brentford at Griffin Park.