Lee Peacock proved the thorn in Martin Allen's side, with goals at opposite ends of the first half. The first was a thumping volley from 25 yards just four minutes into the game at Griffin Park.
He added a second from close range, turning home a curling cross from six yards, on 41 minutes.
Deon Burton's spectacular spinning volley a minute later gave Brentford a crucial lifeline, just before the break, as the sides combined to produce an entertaining, if slightly scrappy encounter.
It survived just four minutes of the re-start, however, as they failed to deal with an inswinging corner, allowing Wednesday right back Lee Bullen to nod home the simplest of headers from a yard out.
Urged on by the consistently vocal and seemingly eternally furious figure of Allen, Brentford managed to exert a degree of pressure in the remainder of the contest, but the Wednesday defence rarely looked unduly nervous.
Young Darren Pratley looked as lively as anything they had to offer when he was brought on with 20 minutes remaining and looks a good prospect for the future.
However it was Brentford substitute Ryan Peters who pulled a goal back with ten minutes remaining, before Stephen Hunt popped up to sweep home on the far post, three minutes into injury time, for a last gasp equaliser.