ATDHE Nuhiu scored a late winner from the penalty spot to pile the misery on shot-shy Middlesbrough.
Aitor Karanka’s side have now gone more than 700 minutes without scoring but had looked good value for a point in a laboured game between two mid-table teams.
They should have been awarded a goal when Jacob Butterfield’s long-range shot on 12 minutes hit both posts and appeared to cross the line before Chris Kirkland retrieved it.
But referee Andy D’Urso waved away the claims.
And it was D’Urso in the thick of the action four minutes from time when he at first he missed the handball by Dean Whitehead that prevented Leon Best’s shot from point-blank range finding the net.
But his assistant referee, Paul Hodskinson, who had not spotted Butterfield’s shot crossing the line in the first half, flagged for the infringement and Whitehead was dismissed.
Nuhiu tucked away the penalty to end a run of three straight home defeats for the Owls.
The victory moves Wednesday up to within a point and place of Boro in mid-table, and more importantly, 12 points clear of the relegation zone and all-but assured of another season in the Championship.
Boro, meanwhile, have not scored now for 704 minutes, since beating Charlton on January 18, but could feel aggrieved at the ‘goal’ that was never given.
They also found Chris Kirkland in fine form, the former England keeper denying Danny Graham one-on-one midway through the second half and Kei Kamara on the rebound.
Sam Hutchinson’s was the best player for Wednesday and drew a wonderful flying save from Tomas Meijas with a 25-yard drive.
“We lost the game because we didn’t play well. I don’t have to put excuses on the referee or linesman. We had four or five chances to score; we had the post chance and Danny Graham and Kei Kamara had very, very clear chances and if we had scored a goal we would have won the game.”
Middlesbrough last scored in mid-January and Karanka said his side’s lack of goals was a worry.
“It’s a big concern for me,” he added. “This team, with the same players, scored a lot of goals in the past. We won five or six games in a row and had a lot of draws.
“We won against Millwall two-nil and against Blackpool. We scored two goals at Bolton, won three-nil at Reading and for this I am concerned because this team is capable of scoring goals and we’re seven games without scoring.”
Sheffield Wednesday head coach Stuart Gray was pleased to secure all three points from an ‘ugly’ game.
“I think we deserved the win,” he said. “The disappointing thing was the first half - there was no intensity.
“One thing you do know is that Middlesbrough are going to have a lot of possession of the ball so we tried nullifying that by pressing them up high but then it was one, two, maybe three touches too much instead of moving the ball quicker.
“If you’d said to me before the game: ‘Play ugly and win one-nil’, I’d have snatched your hand off.”