The visitors took the lead just before the hour mark as Mauro Boselli's header was enough to beat the Forest keeper.
The hosts weren't about to give up, however, and pulled a goal back shortly after half-time through Simon Cox's long-range strike. Forest were handed another slither of hope when Antolin Alcaraz was shown a second yellow card, reducing Wigan to 10 men.
This hope was soon dashed, though, as Callum McManaman completed the victory with a goal in stoppage time.
Wigan will now return their focus to the Premier League as they gear up to face Stoke City on Saturday.