Jeremie Aliadiere pounced in the 89th minute to steal the points for Middlesbrough in a 1-0 victory which left Wigan counting the cost of a catalogue of missed chances.
Aliadiere struck after Stewart Downing nodded the ball into his path with a right-foot shot past Chris Kirkland to give Gareth Southgate's men three points they scarcely deserved.
Wigan had largely dominated with leading scorer Amr Zaki seeing a powerful effort tipped around the post by Ross Turnbull, who also saved well from Wilson Palacios, Jason Koumas and Emile Heskey.
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