A first-half strike from Jonny Howson proved to enough to give Hughton's side all three points, the midfielder netting from distance in the 34th minute.
Norwich went into the game at the Britannia Stadium on the back of consecutive Premier League defeats to Tottenham and Aston Villa respectively, leading to rumours that Hughton's position at Carrow Road could be under threat.
And he is hopeful his side will gain confidence after handing Stoke their first home loss of the campaign.
"This is a tough place to come. We had really good spells were we dominated possession," he said.
"We coped with their threat, we had a bad result last week and we knew it was important to start well. We played with a high tempo and the players deserve everything.
"It's about picking up points and hopefully this will give us some confidence."
Howson's strike marked his first goal of the season, and the former Leeds United man felt that Norwich deserved to win by more.
"I think we deserved it in the end, we kept them to very limited chances, I think we set the tempo with how we started the game," he told Sky Sports.
"We'd had a few chances before that, it always helps when you are on top, it gave us confidence, we could have had a couple more on another day."
‘After Manchester City’s recent form, maybe they’re the underdogs against Manchester United!’ Former Red Devils defender on this weekend’s derby
‘Arteta, Alonso, Emery, me… none of us were physical players – we needed the understanding of the game. That probably helped us move into management’: Premier League boss reveals reasons for natural career progression
