Fletcher's two goals before half-time saw Sunderland recover from a 1-0 deficit and O'Neill was impressed with the striker's performance.
"Fletcher was fantastic," he said.
"It was not just his goals but also his whole centre forward play. We took great heart from his performance."
Wigan piled forward after Angelo Henriquez pulled a goal back with 11 minutes to go, 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 and were never out of it.
"It was all hands to the pump at the end and I am delighted with the result."