In a first half which the hosts were the better side, Swansea took the lead in the 11th minute as Jordan Ayew danced through the Wolves defence before firing beyond Will Norris.
Wolves came back into the game after half time as substitute Diogo Jota scored to level up the scores at the Liberty Stadium.
But it wasn't to be for Wolves as just minutes later, Wilfried Bony poked the ball beyond Norris to send Swansea through to the fourth round of the cup.
Nuno felt that, after a slow first half, his side looked like the team that was going to win the game after the half time interval.
He said, "There are good things and bad things about the game but we will see more from deeper analysis.
"It was a competition in which we wanted to go on and go further but it was not possible.
"First half was not so good and the second half was better.
"I think we were in control of the game when we equalised and it seemed like we were going for the win - I think we were the better team in that moment and the momentum was ours.
"Like always, we will analyse but we have to go and look for the future and the future is just around the corner on Saturday."
It was a cold night in South Wales with torrential rain throughout the game which made conditions difficult for playing football.
Nuno admitted that the conditions were challenging for both sides but he is taking remaining positive as he turns his attention to Nottingham Forest at Molineux on Saturday.
"For both teams the pitch was difficult, it was a tough night and a typical winter night," Nuno said.
"When you lose a game, the first reaction you have is that there are no positives but there are a lot of positives from this game.
"It's about the squad, it's about growing the team and it's about having options for the rest of the season.
"We have to look how many games we have gone without losing a game - now we lose, it must be the same again.
"We have shown again that we really can compete against any opponent - we are ready to compete game by game, this is what I'm looking to improve.
"I want to create an identity that allows us to go to each pitch and compete.
"Today, we showed that we are in the right way. I know it's disappointing and the fans came a long way to support us until the end, but they saw what we are ready to do - the team is ready to compete in any pitch."
