Wigan were the more dangerous side in the first half but Boro stormed back after the break. The Lancashire side, apart from an equalising goal by Yakubu, survived tremendous pressure.
Australia international Mark Viduka returned to the Middlesbrough attack after a lengthy spell on the injured list.
There were a lot of empty spaces around the stadium which suggested the smallest crowd of the season.
Wigan showed threat in attack and Middlesbrough were indebted to Mark Schwarzer for denying Wigan a match-winning lead. Schwarzer's first save was from a Paul Scharner header, a brilliant one-handed stop when a goal looked certain.
Yakubu forced Chris Kirkland into a brilliant save at the opposite end with a close-range header from a Stewart Downing cross.
Yakubu broke through after a one-two move with Viduka. The move broke down and the Middlesbrough fans were not happy that referee Steve Bennett refused to award a free-kick.
The Orpington official awarded Wigan a penalty shortly after for an offence by Emanuel Pogatetz against fellow Austrian Scharner.
It was a correct decision because Pogatetz pushed Scharner off the ball.
Henri Camara took a long time to take the spot-kick. It was as though he was playing mind games with Schwarzer. Camara gave the goal keeper no chance with a low shot into a corner of the net.
This was the third penalty Middlesbrough had conceded in the last four games.
Pogatetz was booked for a foul when he sent Camara sprawling, before Schwarzer brought off a superb save from Scharner after 35 minutes.
The goalkeeper could not have been happy that the Wigan player was completely unmarked so close to goal.
Schwarzer rose to the occasion shortly after against Leighton Baines when he dived full length to push a shot round the post.
But for the heroics of Schwarzer, Middlesbrough would have been dead and buried at this stage.
Just before the break Wigan goalkeeper Kirkland was injured when he dived at a Downing free-kick. Kirkland just got to the ball before Yakubu, but he suffered a head injury in the process.
Wigan prepared to bring on substitute Mike Pollitt but the vastly-improved Kirkland bravely decided to continue.
Pollitt, however, was called in to action for the second half. while Middlesbrough substituted Pogatetz with Stuart Parnaby.
Middlesbrough stepped up the tempo at this stage and Wigan were forced on to the defensive. The visitors, however, covered well against fierce pressure.
An equalising goal was inevitable though and Yakubu supplied it after 66 minutes. He scored from six yards following a right-wing cross from James Morrison.
Wigan brought on Antonio Valencia but pulled him off after just ten minutes due to an injury.
Pollitt then made a brave save at Yakubu's feet while Kevin Kilbane shot high and wide for Wigan.
It was one-way traffic towards the Wigan goal but the Latics refused to panic. They had plenty of bodies in the penalty area as Boro went flat out for a winning goal.
Home defender Abel Xavier had a chance of match-winning glory in the final minute, but he headed just over the crossbar.