Mark Hughes’ men knew a three-point haul would move them above their opponents and into 11th place and they took advantage of some sloppy defending to achieve their aim.
Ryan Shawcross scored right on half time and Peter crouch added a second early in the second half to seal the win which now means the Hornets have picked up just one point from five matches and slip down to 14th spot on 22 points.
Following a slow opening to the game, in which neither side really threatened, Stoke generated the first half-chance in the 16th minute.
Joe Allen pounced on a sloppy Valon Behrami pass in the middle of the pitch and sent Marko Arnautovic clear down the left, but Sebastian Prodl did well to cut out his pass looking to pick out Jon Walters waiting for a simple tap-in.
Stoke continued to dominate possession and almost took the lead on 31 minutes when Crouch got up to meet an Erik Pieters ball into the area and powered a header across the face of goal which Heurelho Gomes had to punch clear.
On the counter-attack Troy Deeney was sent on his way towards goal but took too long over his shot and the chance was gone.
On 33 minutes Jose Holebas played in Abdoulaye Doucoure down the right and, instead of going for goal, he tried to pick out Deeney in the middle and his pass was cut out.
Stoke did take a lead into the interval when Charlie Adam’s stoppage time corner dropped to Shawcross in the area and he flicked in a left-foot effort past Gomes.
Both sides had early chances in the second half with Doucoure hitting a fierce drive from the edge of the area which Lee Grant did well to parry away, before Walters scuffed a shot wide from 10 yards after being teed up by Arnautovic.
However, the hosts doubled their lead on 49 minutes when Adam’s ball into the area from the left was completely missed by Prodl and dropped to Crouch who diverted it past Gomes off his knee.
Both sides pressed to add to the scoreline with substitute Ibrahim Affelay hitting a 30-yard effort which dropped inches wide of the goal on 70 minutes.
Three minutes later Crouch headed the ball down into the path Walters but Gomes bravely made the save to deny him a third goal for the hosts.
On 76 minutes Glen Johnson managed to clear a Jerome Sinclair header off the line, before Prodl headed wide gfrom an Etienne Capoue cross seconds later as Watford pressed for a way back into the game.
With the visitors pushing for a goal, Stoke had a couple of chances to add a killer third goal inside the final 10 minutes but both Walters and Shawcross spurned them.