With new-boy Alfred N'Diaye an imposing midfield presence on his first start, the visitors levelled through Craig Gardner's penalty - Sunderland's first in 34 matches - before Fletcher hit Wigan with a superb one-two.
The Scot clearly enjoys facing the Lancashire outfit as he has now scored six times against them in seven appearances.
His first owed much to his lightning reactions after Ali Al Habsi had turned away his header, with the second an instinctive curling strike from Adam Johnson's lay-off.
"Fletcher was fantastic," said Sunderland boss Martin O'Neill.
"It was not just his goals but also his whole centre forward play. We took great heart from his performance."
At that stage Wigan were inept and staring down the barrel of a big defeat.
But the half-time introduction of midfielder Roger Espinoza triggered an immediate improvement and fellow new-boy Angelo Henriquez made his mark when he scored his first goal for Wigan when he nodded home Shaun Maloney's far-post cross 11 minutes from time.
"I was pleased that they didn't seem like new players," said Martinez.
"They looked like they knew exactly what they were doing.
"Roger is someone with great energy, which he compliments with a real style in possession.
"Angelo is a goalscorer and to score a goal on your Premier League debut is a great boost for his career."
Wigan piled forward after that but Mauro Boselli wasted their best chance when he headed over, leaving the hosts to lick their wounds and O'Neill to praise a backs-to-the-wall effort from his defenders.
"We've had to show a lot of fight and determination," said O'Neill, whose side have moved comfortably into mid-table after five wins from their last eight games.
"Wigan threw a lot at us but and were never out of it.
"It was all hands to the pump at the end and I am delighted with the result."