Fletcher cashed in when he turned home James McClean's driven cross to claim his fifth goal in four Barclays Premier League game.
The Scot's strike was enough to end a run of 12 league games without a win, and O'Neill was delighted.
Asked if his £12million summer signing was proving a bargain, he replied with a smile: "I agree, yes - £35million without a problem, and add-ons.
"He did very, very well. He was brilliant today for us. Wigan came and played their part, and I have to thank Mignolet for making two incredibly good saves for us to keep it at 0-0.
"Fletcher has come up big again for us, so eventually we have won the game, although it was edgy towards the end. But the win was vitally important for us and it keeps us going."