Stoke full-back Erik Pieters scored the only goal of the game, a fortunate cross-cum-shot that looped over Newcastle 'keeper Tim Krul and into the net.
Despite a narrow scoreline, Hughes believes his side controlled the game throughout and were unfortunate to not add more goals to their tally.
"We had a number of clear-cut chances, at least three, and a golden opportunity in the first half when Peter Crouch hit the post after a great ball from Marko Arnautovic," he said.
"I thought it was a good performance. Newcastle came here and turned up with a different game plan and a different shape than we expected - so it took a little time to get to grips with that," he told Sky Sports.
"We felt in control of the game, we felt comfortable. I thought the lads at the back dealt with any threat that Newcastle had today and we were always a threat going the other way.
"(Pieters) does get forward, he gets into good situations and he has done this season where maybe he should have done better. I'm sure he'll claim the goal as one that he meant.
"It was the boost that we needed. I thought that we were value for our lead at half time - we didn't play as well as we can but that's credit to the opposition. In the second half we were more comfortable."
Hughes reckons his team are thriving after a change of playing style, but admits there is still work to be done if they want to compete in the Premier League next season.
"This year, we've took it forward a little bit in terms of what we produce and the fans are enjoying what they see at the moment," he said.
"Our away form, in comparison to our home form, is poor. We need to improve that aspect of our play but if we can do that, we'll be really strong again.
"Maybe people are acknowledging that we play in a different way. You just try and play the game and get good positive results and performances, and at the moment that's what we're doing - we're pleased."
Stoke captain Ryan Shawcross featured in his 200th Premier League appearance for the club, and the Potters boss reserved special praise for his skipper - hoping he can lead a late charge up the league table.
"He'll always give everything when he's playing. He's struggling a little bit at the moment with a hip issue which he's managing day to day - but he always puts his hand up ready to play and play at a decent level," he said.
"The order of the day was to get closer to Newcastle and we've been able to do that - we're only three points away from them.
"I'd like to think our momentum is better than theirs at the moment. If we can keep going, with four games to go, who knows?"