Boro have now gone nine Premiership games without a win, with the latest blow an injury-time winner for Wigan.
Manager Steve McClaren is coming under increasing pressure and there were boos from a section of the crowd when he twice appeared in the technical area.
It was a memorable day for David Thompson and Neil Mellor, Wigan's two transfer window signings. Both got on the scoresheet, with Mellor the last-gasp hero.
Middlesbrough welcomed back England prospect Stewart Downing after a lengthy absence with a knee injury, while former Arsenal midfielder Ray Parlour was also in the starting line-up after recovering from injury.
Wigan, however, struck the first blow with Jason Roberts scoring after three minutes. Thompson and Mellor were involved in the build up before Roberts provided the finish. Home goalkeeper Brad Jones got his hands to the ball but failed to prevent it going into the net.
Wigan played with more purpose and confidence and the Boro defence was all at sea in the early stages. Jones twice denied Roberts, who looked keen to increase his 12-goal tally for the season.
Boro defender Ugo Ehiogu came on as a substitute for the injured Chris Riggott after 27 minutes. It was Ehiogu's first appearance since a transfer to West Brom collapsed because of a disagreement about personal terms.
Wigan doubled their lead after 29 minutes when Gary Teale crossed from the right, and Thompson got in front of Gareth Southgate to head past Jones.
Boro had a chance to pull one back when Downing sent Yakubu through the middle. The Nigerian had a free run but his lob over advancing keeper Mike Pollitt bounced wide.
It was inevitable Boro would raise their game in the second half. Striker Jimmy Floyd Hasselbaink replaced Mark Viduka and quickly made his mark with a headed goal in the 56th minute, though Wigan boss Paul Jewell would have been unhappy with the slack marking.
The home side were lifted by the crowd and in the 66th minute Yakubu, the club's leading scorer, levelled the scores. From a Downing corner Southgate headed the ball into the area and Yakubu had a simple task to score from a yard out.
Middlesbrough were playing with determination and confidence and it was Wigan's turn to defend. Leighton Baines was prominent in defence with Graham Kavanagh always involved in midfield.
Wigan, however, refused to sit back and preserve a point. In injury-time Jimmy Bullard crossed from the right into a crowded penalty area where Roberts back-heeled the ball for Mellor to strike from close range.
Wigan were thrilled, Boro deflated.