Chris Hutchings enjoyed his first win as Wigan boss, but Middlesbrough suffered their second loss in two games as they slumped at the JJB.
Wigan enjoyed the lion's share of possession, but could not penetrate Middlesbrough during a goalless first half.
Jason Koumas had his shooting boots on and his long-range free-kick forced Mark Schwarzer to turn the ball around the post.
But Wigan found the goal their pressure deserved in the 55th minute when Luis Antonio Valencia's firm shot was parried by Schwarzer and Antoine Sibierski was on hand to turn it in from close range.
Stewart Downing did his best to pull Boro back into it, flashing a strike just wide before crashing a fierce drive against the post.
The only solace for Boro fans was the sight of Mido in the directors' box - the Egyptian striker on the brink of a £6.8million move.