League leaders Plymouth struck right at the start and then at the last to stay on top of the table.
Ryan Hardie gave the hosts an early advantage promptly cancelled out by Liam Palmer.
What followed was two League One heavyweights going toe to toe with the visitors well ahead on points.
Twice the Owls hit the woodwork as well as finding themselves up against a goalkeeper in inspired form.
But the knockout blow never came and the Pilgrims landed a late sucker punch through substitute Sam Cosgrove to put Wednesday on the canvas.
An action-packed opening on the South Coast saw two chances fall the way of Hardie – the second of which was converted.
After the striker had a long range effort deflected past the post, Hardie went one better and gave his side the lead inside three minutes.
A swift break upfield from an Owls attack led to Hardie picking up possession 25 yards out on the angle and advancing to fire a fierce drive that whistled into the far corner.
It was the perfect start for Plymouth in a raucous atmosphere – but Wednesday hit straight back to dampen the mood and equalise on seven minutes.
Tyreeq Bakinson looked up to slot a delightful ball through to Palmer, who cut inside and beat Michael Cooper from 12 yards.
The tempo of the game was relentless and Wednesday slowly but surely began to take a grip – Josh Windass was inches away with a wicked free kick from distance that had Cooper beaten all ends up.
The keeper did superbly, though, to deny Windass moments later, getting down low to push a bullet strike in the area on to the woodwork.
The Owls piled on the pressure and Will Vaulks went close, side-footing past the upright after being teed up invitingly by Barry Bannan.
The skipper then played a key role at the other end, bravely diverting a Joe Edwards hit off course as the Pilgrims captain took aim inside the box.
Plymouth finished a frantic first half with a flourish - David Stockdale thwarted Morgan Whittaker with a flying save and Hardie ended as he started, this time finding space in a crowded penalty area to scoop just wide.
Wednesday carved a good chance straight after the restart when Michael Smith scampered clear to advance on goal but the finish was underhit and Cooper gratefully gathered.
Windass could be forgiven for thinking it was not his night as he struck the woodwork for the second time. Cooper could only watch as the ball flew by from 20 yards and fortuitously landed in his grasp off the post.
Marvin Johnson was next to threaten, motoring down the left flank and coming in to unleash a rising shot that Cooper did well to push over the bar at full stretch.
Both goalkeepers then rose to the fore with superb saves to keep the score level.
Cooper denied Palmer a second goal with a stunning reflex stop before Plymouth countered in a heartbeat and Stockdale kept out a fizzing shot from Adam Randell.
And still there was a grandstand finish to come but in devastating fashion for Wednesday.
After Michael Ihiekwe hooked Dan Scarr’s header off the line, it seemed the points were set to be shared.
But a minute into stoppage time, Plymouth poached the winner. A smart cross from Bali Mumba saw Cosgrove get a perfect connection to make the long journey home one of some frustration for the travelling Wednesdayites.
Wednesday: Stockdale, Palmer, Heneghan, Ihiekwe, James (Iorfa 46), Johnson, Vaulks, Bakinson (Gregory 89) Bannan (Dele-Bashiru 73), Windass (Paterson 73) , Smith