Mark Warburton's side recorded a fourth-successive win as two goals in the final nine minutes subjected Fulham to a first league defeat since Kit Symons took full control last month.
A tense first half failed to produce a goal, but three minutes before the hour Fulham took the lead through Hugo Rodallega, the Colombian converting Ross McCormack's cross.
Their lead lasted until the 81st minute as Brentford's pressure finally told, Harlee Dean firing a Stuart Dallas delivery into the top corner from the edge of the penalty area.
With full time approaching, and a draw looking likely, Brentford snatched all three points as Jota Peleteiro's strike deflected off Dan Burn in stoppage time.
After two games without a win Russell Slade's side got back to winning ways thanks to two goals in the first half, with Reading defender Alex Pearce having 45 minutes to forget.
