Two goals from Fletcher before half time saw Sunderland completely reverse the scores, with the Scottish striker netting his first in scrappy fashion after Ali Al-Habsi had saved his initial shot.
A smart pass from Adam Johnson found Fletcher in space inside the box and the forward doubled his personal tally with a powerful finish into the top corner.
Wigan looked a much-improved side after the interval and Shaun Maloney went close to pulling a goal back after bursting through the visiting defence but Mignolet reacted to push the ball to safety.
Sunderland continued to live dangerously as Wigan pushed for a way back into the match to avoid dropping into the relegation zone.
Angelo Henriquez headed home powerfully at the back post to score Wigan's second and set up a dramatic finish but Sunderland held firm to secure the victory.