Hughton admitted his side should have added to Anthony Pilkington's opener as they bossed the opening half, and Shaun Maloney levelled the scores just after the break.
But a rare header from the diminutive Wes Hoolahan proved enough to earn another three points for the Canaries.
"I'm really delighted because Wigan are a very good side and play a similar system to Villa," Hughton said. "They pass the ball very well and when they got their equaliser early in the second half we had to show great character.
"We had to get back in the game and make sure that we had a good period ourselves, and I think we weathered it a little bit and came strong.
"Certainly over the game we had the better chances, and should have really made it a bit more comfortable for ourselves.
"We had really good opportunities to be further ahead at half-time. Their goalkeeper had to make a couple of very good saves, but Wigan showed why they continue to be in this division.
"They pass the ball very well, they have a system of playing that gets them in the opposition's final third, and they have got quality. We had to match that today.
"I thought we were very, very good at times. Yes we could have made it better for ourselves in that first half, but that's the game. Then we had to get back into it, but in the end I think we got a deserved winner. It wrapped up a really good performance from us."