Jean Beasejour's first-half goal was cancelled out by Davide Santon with 18 minutes to go only for Arouna Kone to snatch a vital close-range goal in a goalmouth scramble for Roberto Martinez's relegation-threatened side.
The win was crucial for third-bottom Wigan after both Aston Villa and Southampton won at the weekend.
"It was just a huge effort from us to try and go and get the winner and we were a bit unfortunate in the end, but that's a massive three points for us," the man of the match told Sky Sports.
However, the striker believes Callum McManaman's tackle on Massadio Haidara was 'not that bad' when he first saw it.
He added: "At that split second I didn't think it was that bad. Obviously coming off at half-time they (Newcastle) were very angry, so you can imagine it obviously wasn't great but actually on the pitch at the time, it didn't seem anything ridiculous."
Asked if he thinks this win could be the start of another great escape, Maloney said: "We hope so. It's disappointing that we're in this position again, but we found ourselves in it and it's up to us to get ourselves out of it."