Stewart's goal was surrounded by controversy as Wigan players and fans first of all thought the ball had gone out of play, but when the linesman waved play on and the cross came over an offside looking Stewart prodded the ball past John Filan.
The goal stunned the home fans in the biggest football crowd seen in the town since 1953, but Sunderland danced jigs of delight as the three points almost guarantees them promotion to the Premiership.
To be fair Sunderland looked the better side throughout with their passing crisper and more accurate than that of a Wigan side which failed to recover from Saturday's home defeat against West Ham.
Chances were few and far between, but Wigan might easily have gone in front even before Sunderland's opener when Gary Teale saw his shot parried by Thomas Myhre.
Jason Roberts and Nathan Ellington also went close as Sunderland defended what they had but they too might have added a second had Filan not made a smart save from Dean Whitehead.
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