Oldham's first home win for over two months ended in controversy after keeper Les Pogliacomi was sent off in stoppage time for violent conduct.
The big Australian allegedly elbowed Bees midfielder Steve Hunt but his manager Iain Dowie was livid at the decision.
Dowie insisted the two players were simply jockeying for position at a throw-in before Hunt collapsed clutching his face, prompting Pogliacomi's straight red card.
Dowie blasted: "There's no way Les would elbow somebody, it is not in his nature.
"There was not a mark on their player and Les was just trying to reach across a much smaller lad.
"I don't want to take anything away from my team though because we played some great stuff in the first half and our front two were outstanding.
"Ben Burgess had a very good debut and Chris Killen was excellent. I have not understood some of the criticism of our home form and I think we proved a point." Brentford manager Wally Downes said: "I'm sure the ref handled things as best he could. Our problem was that we did not play well enough.
"We had to change our system and the lads did not handle it - we could have had Maradona out there and he would have looked useless as well." Oldham went in front with their first chance as Darren Sheridan's corner was headed into the top corner from ten yards by defender Fitz Hall.
But Brentford soon levelled as a defensive mix-up allowed Kevin O'Connor to sneak in and beat Pogliacomi from the edge of the box.
Burgess missed a clear opening before helping set up the winner just after half time with a clever flick.
Chris Armstrong crossed from the left and skipper Lee Duxbury pounced with a close-range header.
Oldham held on comfortably but Dowie ended the night furious with the referee.