Ryan Shawcross sent the hosts into half-time with the lead after striking home from inside the area three minutes into additional time.
Peter Crouch managed to turn Charlie Adam’s cross home from close range on 49 minutes for the 98th Premier League goal of his career.
Both sides created chances in the second-half, but Stoke managed to see out the game to complete the league double over the Hornets.
Gomes denies Crouch with fine save
Both sides lacked a cutting edge inside the final third before the Potters tested Heurelho Gomes for the first time.
Erik Pieters hung the ball up for Crouch at the back post, and the former England international nodded at goal and forced Gomes into making a full-length save.
Watford should have then done better with their first chance on 34 minutes, Jose Holebas held the ball up well before sliding the ball through to Abdoulaye Doucoure.
The midfielder had a clear sight of goal, but instead of taking the shot and forcing a save out of Lee Grant, he decided to pull the ball back for Troy Deeney and Stoke managed to clear the danger.
Stoke strike either side of half-time
The game looked set to be goalless at the break, but the hosts had other thoughts as they broke the deadlock in the third minute of additional time at the end of the first-half.
Charlie Adam’s corner bounced before reaching Shawcross, who wrapped his foot round the ball and rifled into the net to send the Potters into half-time with the lead.
It was the hosts that came out after the break and almost found themselves level as Doucoure’s curling effort was pushed away by Grant.
The hosts went and doubled their lead soon after, just four minutes after half-time, and again, questionable defending was to blame for the visiting side.
Adam picked up the ball and put a delightful ball into the box, and Crouch came sweeping in and tapped the ball into the net for his 98th Premier League goal.
Potters close to finding third goal
The next chance fell the hosts way on 71 minutes, Adam’s cross was half-cleared by Younes Kaboul and substitute Ibrahim Afellay strikes just wide of the post.
Watford had two chances in quick succession soon after, firstly, substitute Jerome Sinclair saw his driving effort cleared off the line.
The ball made its way out to Etienne Capoue, who crossed and Sebastian Prodl glanced the ball on inches wide of the far post.
Stoke could have asserted themselves further seven minutes before time, Jonathan Walters broke through, but Gomes produced a strong save to push the ball behind.
The resulting corner took a ricochet and fell to Shawcross, who slashed across goal and the ball flew just past the far post.