Aliadiere's first league goal this season secured Middlesbrough the win
Jeremie Aliadiere scored an 89th-minute winner to give Middlesbrough their first away league victory of 2008 at the expense of Wigan.
The hosts dominated for long periods but were denied by an outstanding defensive performance from Boro.
Amr Zaki saw a first-half strike well saved by Ross Turnbull, who later thwarted Emile Heskey in fine fashion.
Boro pressed forward late on and Aliadiere rounded off a superb move with a cool finish at the death.
It was a result that, by and large, came against the run of play but one that rewarded a spirited display from a side desperate for a win on the road.
The victory edged Middlesbrough away from the relegation zone and handed Wigan their first defeat since the opening day of the season.
Southgate was pleased with a tough win for his side
Steve Bruce, his players and their supporters looked stunned at the final whistle and they go into the international break on eight points, one less than the manager had stated as his target.
Considering Wigan arrived unbeaten in their last four league games and Boro with four defeats from as many outings in all competitions, it was hardly surprising that the Latics made the brighter start.
An ankle injury to Andrew Taylor meant Boro boss Gareth Southgate was forced to recall Jonathan Grounds from his loan spell at Norwich and throw him straight into the starting XI at left-back.
But the 20-year-old looked ill at ease when confronted by Antonio Valencia and his problems were compounded by Mario Melchiot's willingness to overlap from right-back and Heskey's inclination to drift over to Boro's left side whenever possible.
Inside 10 minutes, Heskey rose highest to flick a long ball into the path of Wilson Palacios, only for the midfielder to drill his shot across the face of the goal and, soon after, Zaki could only find the side netting from Valencia's deep free-kick.
Boro were playing with the confidence of a team that has not won on their league travels since 29 December, 2007.
Wigan, who came into the game without back-to-back league wins since August 2007, were probing on both wings and Olivier Kapo, stepping in from the left, began asking serious questions of Justin Hoyte.
But Boro, marshalled superbly by David Wheater and Chris Riggott in central defence, held firm and provided a solid base from which the visitors could begin to attack.
With Aliadiere and Stewart Downing hugging the right and left touchlines respectively, and Afonso Alves and Mido requiring attention in the middle, Boro were able to stretch Wigan on the counter-attack.
One such move on the half-hour mark allowed Gary O'Neill a sight of goal and his 25-yard drive was deflected behind for a corner by Titus Bramble.
That marked a rare period of pressure from Boro and two minutes later Mido's cross from the right was headed narrowly wide by Wheater after the centre-half came up from the back to out-jump Bramble.
Bruce said his side were 'mugged' by Boro
Wigan finished the first half as they started and a neat interchange by Palacios and Heskey allowed Zaki to unleash a fierce goal-bound strike that was expertly tipped around the post by Turnbull diving to his right.
Just after the break Valencia teased Grounds before seeing his shot repelled by Turnbull. The ball fell kindly to Palacios but the Honduras international, still awaiting his first Wigan league goal, blasted his effort over the bar.
Palacios's miss epitomised a largely disjointed affair, as did the first touch of Didier Digard, who was fed by Aliadiere moments after replacing Mohamed Shawky but knocked the ball too far and was foiled by Chris Kirkland.
Desperate to break his Premier League duck, Palacios was twice denied by Turnbull with shots from outside the area as Wigan attempted to increase the intensity.
Wigan dominated possession but met a determined Boro side
But Middlesbrough's defending as a collective unit was first class and the performances of Riggott and, in particular, Wheater will have been keenly noted by on-looking England manager Fabio Capello.
Heskey's close-range volley from Henri Camara's header was brilliantly blocked by Turnbull but otherwise Wheater negated the England striker's threat.
And that allowed Boro to go in search of a late goal, which duly arrived when Digard's cross from the right was cushioned into the path of Aliadiere by the head of Downing.
The Frenchman took one touch and then slotted past Kirkland with aplomb.
Wigan manager Steve Bruce: "In the opening exchanges they did not get a kick so they had to change their formation.
"When you are in the ascendancy like that you have to score and we did not.
"We did not deserve to get beaten and we would have settled for a 0-0 draw.
"We have been mugged in the last minute and that is frustrating."
Middlesbrough boss Gareth Southgate: "We rolled our sleeves up and were tough mentally and we deserved something from the game because we took our chance.
"The irony is that we played better in the previous two games and got nothing from them.
"This has been a hard period because we have had a lot of games away from home.
"We have had several good performances but with no reward, but this gives us confidence going into the international break and then we will face Chelsea."
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