The midfielder bundled home his shot to beat Hartlepool's gallant keeper Jan Budtz seconds before the game was destined for penalties.
Wednesday shook off their grim league form to dominate the first half but failed to make it count despite keeping the visitors under pressure.
The Yorkshire side, bottom of the Championship thanks to a hat-trick of league defeats, were within a whisker of a fourth-minute opener when Marcus Tudgay and Deon Burton linked well before Glen Whelan forced a smart save from Budtz.
As Wednesday maintained the pace Frankie Simek aimed a cross from the right that found Tudgay but his eye-catching volley went wide.
Then Simek burst in from his right back position with a lightning run and finished off with a low shot that Budtz parried and Burton O'Brien's follow up was held by the keeper.
Seconds later Tommy Spurr's shot beat the Hartlepool keeper but Gary Liddle was well positioned to clear off the line before a Kenny Lunt shot went wide.
A Tudgay header was high before another great run by Simek had the visitors backing off before the American defender hit a searing low drive wide.
Hartlepool left it late in the half before they created a threat that had Wednesday worried. Clever work from substitute David Foley and Liddle set up James Brown 12 yards out but he swung and missed the ball as it skidded across the area.
But nine minutes into the second half Hartlepool went ahead with their second chance of the night when Brown whipped in a cross from the left and Ian Moore rammed the ball home.
The lead lasted just 14 minutes before Wednesday were level thanks to captain Burton who drilled a low shot throw the legs of Budtz after a superb crossfield pass from Jermaine Johnson.
Budtz was the hero again in the 74th minute when Tudgay looked certain to claim the winner with a close-range shot but he was denied by a last-ditch block.
And in the 89th minute Johnson was denied a Wednesday winner when a stunning 20 yarder hit the upright.