The striker got across his man at the near post to power a header into the roof of the net and deny Brentford keeper Daniel Bentley the clean sheet a string of breathtaking saves deserved.
The late leveller cancelled out Lasse Vibe's opener after 54 minutes when he chased down a lost cause and blocked keeper Keiren Westwood's clearance to roll the ball into the empty net.
It was the classic game of two halves at Griffin Park in a clash that had everything, with Wednesday dominating before the break and Brentford resurgent in the second 45.
Both sides ended with 10 men in a game that was niggly rather than dirty, with David Jones seeing red for the visitors on 73 minutes and Vibe for the hosts with two minutes remaining, both for two yellows.
The visitors dominated a one-sided first half that should have seen them go in at least three to the good at the break.
Only Bentley in the Brentford goal kept livewire strikers Steven Fletcher and Fernando Forestieri at bay with a succession of breathtaking saves.
And the Owls also had Lucas Joao to blame for an astonishing miss when he contriver to place the ball over the bar from almost on the line with the goal gaping.
Wednesday went close after 12 minutes when Daniel Pudil's drifted cross to the far post was met on the half volley by Forestieri but the effort flew inches wide of the far angle.
Kieran Lee's free-kick on 23 minutes caused the home defence problems, but Tom Lees' far-post header was cleared off the line by a back-pedalling Nico Yennaris.
Joao should have given the visitors the lead to finish of a flowing four-man move, but with the goal gaping and only the slightest touch needed, he somehow chipped over when it looked harder to miss.
That howler, which made Ronnie Rosenthal's famous miss look like a hard chance, was followed by an opportunity for Forestieri who raced clear down the left and fired in a low drive that Bentley got down smartly to stop.
Brentford's first worthwhile effort on goal came on the half hour, John Egan's goal-bound far post header blocked by a melee of Wednesday legs.
Bentley came to the Bees' rescue again a minute later when he showed brilliant reflexes to palm his own defender Yennaris' back header to safety.
The mad five minutes ended with Brentford skipper Harlee Dean clearing Fletcher's bobbling effort off the line as Dean Smith's side struggled to cope with the visitors' quality.
Forestieri went close just before the break before Bentley again kept the score deadlocked with another reflex save to keep Joao's header out almost on the whistle.
But after the interval Brentford stormed back into the game and looked far more competitive in midfield.
Vibe's persistence broke the deadlock and gave Smith's side confidence, and it was Westwood who redeemed himself minutes later when he blocked Scott Hogan's deflected shot with his legs inside the post on the hour.
Hogan twice went close before Yennaris forced Westwood into a full-length save, but Wednesday always looked potent going forward.
Bentley saved one of his best stops for late on when he denied Almen Abdi's snapshot with a reflex save and then tipped Forestieri's header onto the post.
But there was little he could do about the equaliser as his defence switched off for the first time in the 95 minutes and got punished.