Midfielder Charlie Adam's first goal since November 24, 50 seconds into the second half, was enough as Stoke claimed back-to-back wins for the first time in four months.
The Canaries' latest slice of away-day misery - they have only won once on the road in the league all season - should have been tripled but for Peter Crouch missing two embarrassing second-half sitters.
In failing to test Stoke goalkeeper Asmir Begovic even once, Norwich find themselves just six points above the relegation zone and still looking over their shoulders.
Hughton said: "We were up against a Stoke side at their most direct and most physical.
"But you know what you are going to get when you come here and I don't have too many complaints. It's something you have to deal with.
"I thought, if anything, they would get even more direct in the second half and we would have our chances.
"But to concede so early in the second half really hurt us and with this defeat it means we've still work to do.
"We've two home games, which is a plus, and the situation is still in our hands."
- Sports & Recreation
- Asmir Begovic
- Charlie Adam