Jeremie Aliadiere emerged as Middlesbrough's unlikely hero with an 89th minute strike at the JJB Stadium to give his struggling side three points their performance barely deserved.
Gareth Southgate's men had come under increasing pressure from the buoyant home side with goalkeeper Ross Turnbull keeping them in the match before Aliadiere pounced to drill home Stewart Downing's header in the box.
The Frenchman had been a virtual passenger up to that point as Boro, reeling from last week's dismal home loss to West Brom, were made to look distinctly second best.
Turnbull had denied the Barclays Premier League's leading scorer Amr Zaki with a brilliant finger-tip save in the first half and also denied Wilson Palacios, Jason Koumas and Emile Heskey as the home side pressed.
But for once it was Southgate who was left celebrating after a hard-luck start to the season as Aliadiere ended a poor run of personal form by firing home, to the delight of the massed ranks of Boro fans behind the goal.
Coming off last weekend's superb win over Manchester City, the Latics had brimmed with confidence for most of the afternoon, Mario Melchiot almost finding Titus Bramble in the box with a fifth minute cross.
Then Palacios played a clever one-two with Heskey to burst into the Boro box where the ball finally ran away from him as Boro, conversely, played like a team with the home defeat to West Brom still on their minds.
Zaki posed a constant threat and came close just past the quarter-hour mark when he picked up Antonio Valencia's free-kick at the far post but could only steer it into the side-netting.
The game degenerated into a rather lifeless affair although Zaki remained at the center of almost everything, lashing another speculative effort high and wide in the 27th minute.
Heskey, searching for his 100th Premier League goal, was ruled narrowly offside when put through by Palacios then Boro fashioned their best chance to take a lead their performance did not really merit.
With Wigan caught clearing their lines after a Boro corner, Mido swung a high ball back into the box which David Wheater met with his head and directed his shot inches over Chris Kirkland's bar.
Zaki was the first man in referee Martin Atkinson's book in the 37th minute for barging over Mohamed Shawky on the edge of the Boro box, followed by Lee Cattermole for hacking down the same man two minutes later.
Zaki had the best chance of the half three minutes before the break, when he lashed a right-foot shot from the edge of the box that Turnbull did well to tip around the post.
The home side continued to look most likely to break the deadlock at the start of second half, Palacios firing wildly over the bar after Chris Riggott deflected an effort by Valencia into his path.
Heskey curled a long-range effort just the wrong side of the upright and, with both sides continuing to squander possession too easily, the disjointed action was lacking any kind of rhythm.
Downing hit a long-range effort over the bar as if to signal how short of ideas were Boro, whose boss Southgate made his first change on the hour when Didier Digard replaced the injured Shawky.
A slip by Downing set up another Wigan chance in the 67th minute, Valencia neatly setting up the impressive Palacios, who hit a rising shot straight at Turnbull.
Bruce responded by bringing on Koumas for Olivier Kapo and the Welshman sent in a dangerous 77th minute free-kick which almost found the head of Paul Scharner in front of goal.
Koumas was injecting more creativity into the Wigan attacks and embarked on a rangy cross-field run in the 80th minute which ended with a powerful shot which Turnbull saved at full-stretch.
Heskey's toe-poked effort goalwards blocked at point-blank range by the alert Turnbull before substitutes Daniel de Ridder and Henri Camara combined, with the African forcing another brave stop from the goalkeeper.
Then, just when Boro looked like they would be happy to cling on for a point, they seized the win when Downing nodded the ball into the path of Aliadiere - who squeezed the winner low past Kirkland.
