The Potters took the lead through Darren Fletcher, as a rehearsed corner routine found the Scot on the edge of the box and he was able to fire past Heurelho Gomes.
Watford applied the pressure, especially late on as they went in search of an equaliser but Stoke were able to hang on for a vital win.
Speaking after the game, Hughes said: "It was a great performance from us, particularly as the away side, we had a gameplay today and executed it to absolute perfection, which maybe hasn't been the case in the two fixtures prior to this one."
"We looked at what they do and what they like to do and we managed to nullify their threats,” the Welshman said, “and look very dangerous on the break at the other end too.
"Over the course of the 90 minutes I think it is fair to say that we had by far the greater opportunities to score goals,” despite Watford posting higher Expected Goals numbers (according to Infogoal) “not least Charlie [Adam] at the end who managed to hit the post with the goal at his mercy."
How the goal came about
Hughes was quick to divert praise over the set-piece routine to his assistant, Mark Bowen.
The manager said: "We practised it, believe it or not, because a lot of people would have you believe we don't actually work on set-pieces, but clearly we do,
"We could see that they like to pack the six-yard box with bodies on set-pieces,” the 53-year-old said, “particularly corners, so we wanted to get the ball out to the edge of the box and hope we could make something happen that way."
Watford have conceded the most goals from set-pieces in the Premier League this season, something Hughes’ opposite number Marco Silva will need to sort out.
Hughes continued: "I have to say that the first couple of attempts at it in training didn't place a great deal of good will in our hearts to be perfectly honest.
"Thankfully though, Darren has caught it incredibly sweet when it really mattered to win us the game,” the Stoke boss said, “and his goal side, like everybody else, I thought he was absolutely top drawer today."