A late strike from second-half substitute Charlie Adam ensured the victory for Hughes' side who ended an impressive season in ninth place with a record 50 points to their name.
Gareth McAuley put through his own net to give the visitors a first-half lead, but Stephane Sessegnon levelled with a cool finish before Adam struck from outside the box to seal the win.
It was an end-to-end encounter, with both sides hitting the woodwork, but Hughes was delighted to have capped his debut season in charge with another win.
"We allowed them back in at 1-1 and you think that you've missed an opportunity, but we made a change," he told Sky Sports.
"Charlie came on, it was a great strike and we won the game and it's a huge achievement for everybody connected to Stoke.
"We've hit 50 points - our biggest total - and we're in ninth so it's been a great day.
"All in all, we're really pleased with the season that we've had. It's been quite remarkable really what we've been able to do in terms of the way we play now and the points on the board we've been able to achieve. Fifty points in any season is a really good return.
"We've raised expectations but I've said for a long time that I'm okay with that. I think people want to be positive about people's chances and their own team's chances.
"We've done really well this year. Can we beat it? We know it'll be tough but we'll certainly try next year."
Asked if he would now be looking to boost his squad during the summer transfer window, Hughes insisted that any new additions must fit the right criteria.
"I think you saw today by the manor of some of our play that we're very close," he said.
"We'll try and add a little bit of quality if we can and if it's available and it's realistic in terms of the finance that we can put towards it, but it's not a case of wholesale changes, certainly not.
"We've got a good group here and everyone's worked exceptionally hard this year along with the support staff who have been absolutely outstanding.
"It's been a real team effort so I'm really pleased that we've been able to have a season for our fans as well. They came in their thousands today and were absolutely magnificent as they always are so it's really important that we've been able to send them home looking forward to a good summer."
After the travelling fans once again voiced their backing for captain Ryan Shawcross to make the England squad, Hughes reiterated his stance that Stoke players have not had the chances they deserve for the national side.
"I've gone on record and said that I think it's a bit strange that we don't get a mention in terms of our players for England," he said.
"We're ninth in the Premier League and we've done it without any sort of focus on what we're doing and the players that are playing exceptionally well to help our cause.
"Ryan has been outstanding from the first game to the last and he seems to be overlooked. He's not going to get in the World Cup squad.
"If he maintains his form next season, I think it's only a matter of time before he gets his chance and rightly so."