A first half largely dominated by the Potters saw Watford come out for the second half and score twice in four minutes as Troy Deeney gave the Hornets the lead from the penalty spot and Ismalia Sarr doubled their advantage.
Steven Fletcher cut the Watford lead in half in the 83rd minute, but it wasn't enough as Stoke remain eighth in the table on 37 points.
Story of the game
Stoke had the first chance of the match in the 11th minute as Jack Clarke saw his cross headed away by the Watford defense, but the ball came to John Obi Mikel, whose effort took a deflection and went out of play.
Another chance came for the home side, Nick Powell holding the ball up well and releasing it for Joe Allen, his shot sending Hornets goalkeeper Daniel Bachmann flying, but Adam Masina got in a key block.
Despite not seeing much of the ball in the first half, the visitors nearly took the lead on 31 minutes as Will Hughes picked out Nathaniel Chalobah and his rasping shot from 15 yards was pushed around the post by Stoke keeper Joe Bursik.
Four minutes later, James McClean sent in a poor free-kick that Sam Clucas met and hooked it a foot over the bar. Powell then fed Allen, who flashed it across the face of goal where Clucas met it a fraction too late.
In the 52nd minute, Allen took advantage of a poor defensive header by Kiko Femenia and squared for Allen, who forced a brilliant save from Bachmann with a side-footed effort.
Against the run of play, Watford took the lead in the 64th minute. Deeney sent a ball into Sarr, forcing Bursik into a save, but as Joao Pedro raced onto the loose ball, the Stoke keeper took him down. Deeney stepped up to score his second penalty in as many games.
The lead was doubled in the 68th minute as Deeney turned provider, a lovely ball onto the right for Sarr, who collected and rifled a low, angled shot past Bursik to make it 2-0 to the visitors.
Stoke tried to claw their way back into the match as Bachmann saved from Clarke's 25-yard curler. Seven minutes from time, the excellent Allen clipped a ball in for Fletcher, who hooked it over the line before Watford's defense could react.
The Potters had three clear chances to rescue a point in stoppage time, Powell slicing his effort wide, Fletcher sending in a simple overhead kick inside the box and Harry Souttar heading past the post as Watford hung on for three vital points.
Man of the match: Troy Deeney
He turned the match in Watford's favor with his penalty after Stoke dominated the majority of the game up to that point and he turned provider on the Hornets' second goal that ultimately made the difference.
Deeney is still the key to Watford's success
For all of the talent that has come and gone at Vicarage Road, it's still the Hornets' skipper who is the engine that drives the club. His penalty was his eighth of the season and 149th in a Watford shirt and if the club are to make an immediate return to the top-flight, it'll be Deeney that's at the heart of it.
Stoke failed to make all of their possession count
The Potters had 58% of the ball, 14 shots, eight corners and made 15 interceptions yet they couldn't take advantage of all of that dominance and were left playing catch-up after Watford struck twice midway through the second half. With just one win in their last ten matches, the Potters need to make these performances pay off sooner rather than later.