A disappointing 2-0 defeat at Ewood Park has left a big dent in Latics' aspirations for European qualification next season.
Headed goals from Benni McCarthy, on the stroke of half-time, and Ryan Nelson, on the hour mark sealed Wigan's fate as their Lancashire rivals, and in particular goalkeeper Paul Robinson, did enough to earn the win.
Despite some good chances falling the way of Steve Bruce's men they either ran out of ideas in the last third of the pitch or were denied by last ditch defending and heroic shot-stopping.
No sooner had the game started when Antonio Valencia, who worked hard all afternoon, found space in the opposing area and fired towards goal, only for his shot to get a slight deflection and rebound off the bar.
It seemed as though that opportunity would be the cue for a promising afternoon, but instead it was the start of Wigan's frustrations.
With players finding little room to manoeuvre in the final third they couldn't break down Blackburn's back-line and although Amr Zaki was introduced at the start of the second-half he couldn't turn his side's fortunes despite putting in plenty of effort.
The game was summed up shortly after Rovers had doubled their lead when Emmerson Boyce and Valencia had efforts spectacularly saved by Robinson following a Ben Watson corner, and a resulting goal-mouth scramble ended with a goal-kick.
A similar incident occurred minutes before the final whistle with Titus Bramble and Olivier Kapo having their chances cleared away from Blackburn's defence.
Far from being an entertaining game at Ewood Park, and one Bruce will want to get out of his team's system before next week's home clash against Bolton.
