Wanderers’ proud unbeaten record came to an end as they paid the price for a late first-half lapse to hand Wednesday the points.
Two goals in four minutes did the damage as the Owls became only the second team to leave the University of Bolton Stadium as winners since early January.
George Byers and captain Liam Palmer got the goals as Ian Evatt’s men lost for the first time this season and the first time in 13 League One games.
But the Whites will feel the defeat was largely self-inflicted as the hitherto best defensive record in the division was undermined by a sloppy opening goal for Byers which was quickly followed by a rare Palmer strike to give the Owls the platform to go on and see out a victory which lifted them above Wanderers in the table.
Evatt - whose side should have turned an impressive start into a lead of their own - brought back Ricardo Almeida Santos following the defender’s one-match ban as they reverted to the starting line-up that had secured a point at Port Vale a week ago.
And Santos was instrumental in a bright start from Wanderers as he threatened to unlock the Wednesday defence with a couple of teasing passes from the back.
It was high-quality stuff from both sides as they probed for an opening in a cagey first half-hour which then gave way to a manic few minutes which proved costly for the Whites.
Wanderers should have led themselves but instead found themselves 2-0 down with two goals inside four minutes giving them a mountain to climb.
Conor Bradley was again one of the Whites’ most instrumental figures and he nearly capped another eye-catching start with a superb solo goal as a weaving run into the box was stopped only by Michael Ihiekwe’s immaculately timed block.
The teenager then threatened again as he nipped in to intercept a square pass from Dominic Iorfa but with just David Stockdale to beat, steered his attempted finish wide of the target.
And from nowhere, Wednesday were suddenly handed the lead.
Santos hadn’t put a foot wrong but then passed blindly back towards a goal vacated by keeper James Trafford.
Trafford recovered to hook the ball off the line but the Whites never managed to re-set and when Barry Bannan retrieved the ball to pick out Byers, the midfielder slotted home.
That goal – the first they had conceded at home in the league this season – rocked Wanderers.
And moments later they found themselves 2-0 down, Josh Windass playing a lovely pass for the over-lapping Palmer to mark his 350th appearance for the Owls with a tidy finish as the far post.
Wanderers’ long unbeaten record was under threat and there would almost certainly have been no way back had the visitors added a third six minutes into the second half when Windass somehow scooped a close-range effort over the bar from Byers’ ball across the six-yard box.
Inevitably, a physically powerful Wednesday side weren’t willing to give an inch and with half an hour to go Evatt re-jigged his strikeforce to try and light a spark and find a way back into the game as the fit-again Dion Charles made a welcome return.
An Iredale free-kick forced Stockdale into a save and Kyle Dempsey then skidded a low strike just wide after good work from Bradley and Dapo Afolayan as picked up the tempo.
A goal would have re-energised most in an excellent crowd of over 22,000 and raised hopes of a dramatic late fightback.
And Evatt did what he could to try and engineer it with a further triple change as he utilised all five substitutes.
A save at the feet of Wednesday substitute Dennis Adeniran by Trafford kept the deficit at two but despite throwing men forward and plugging away, the Whites couldn’t find a way through to repair the earlier damage.
Wanderers: Trafford; Jones, Santos, Johnston; Williams; Bradley (Sadlier 78), Morley (Charles 61), Dempsey, Iredale (John 78); Afolayan (Kachunga 78), Bakayoko (Bodvarsson 61). Substitutes: Aimson, Lee, Kachunga.
Booked: Bradley, Sadlier
Sheffield Wednesday: Stockdale; Iorfa, Ihiekwe, McGuiness; Palmer, Byers, Bakinson, Johnson; Bannan (Vaulks 90); Windass (Adeniran 82), Gregory. Substitutes: Dawson, Brown, Henegan, Paterson, Dele-Bashiru.
Booked: Adeniran
Attendance: 22,023 (Wednesday 4,754)
Referee: Charles Breakspear