The hosts were twice ahead in a game they needed to win, but were pegged back thanks to a defensive howler.
Alex Pritchard gave Brentford the advantage just after the half-hour but Adam Le Fondre equalised. Jonathan Douglas restored the lead but James Tarkowski’s error gifted a second leveller to Mark Davies.
Brentford lacked the fluency and flair that has got them to the fringes of the play-off chase and looked jaded in the face of a physical Bolton outfit.
Referee Carl Boyeson did little to calm a charged atmosphere at Griffin Park, allowing a string of challenges from the visitors to go unpunished including a two-footed lunge from Emile Heskey.
The Londoners were always looking to play their football and Pritchard twice went close with early dipping free-kicks.
Bolton looked dangerous against a square Brentford back four and Tarkowski had to clear Liam Feeney’s bobbling angled drive off the line.
Former England striker Heskey also forced a fingertip save from Button when he skipped past the home defence inside the first 10 minutes.
At the other end Gray came close to replying to Le Fondre’s equaliser when he turned his man on halfway and raced on to fire a rasping drive against the far post and out.
The opener came when when Andre Gray broke down the right and crossed for Alan Judge, who found Pritchard at the far post to fire home.
But Brentford held the lead for just four minutes, Heskey playing in Le Fondre to slide home from an acute angle with the Bees defence flat-footed.
Mark Warburton’s side edged into the lead again just before the break when Douglas powered a header back across Trotters keeper Adam Bogdan and in off the post from Judge’s pinpoint cross.
After the break both sides settled into a physical war of attrition, with the midfields holding sway as the Bees poured forward looking for the winner and Bolton packed their defence.
Douglas forced a save from Bogdan before Brentford were rocked by a second Bolton equaliser. Davies pounced on an underhit Tarkoswki back-pass to slot home into the empty goal.
Jota’s low cross to the far post was inches away from being turned home by substitute Stuart Dallas and centre-back Harlee Dean was thrown up front for the final 10 minutes as Brentford desperately searched for the winner, but Bolton stood firm.
Defeat leaves Brentford three points outside the top six with two games remaining.