The Potters took the lead early on through Steven Fletcher, but the Hornets were given a route back into the game with a contentious goal awarded to Tom Cleverley. Brazilian forward Joao Pedro then gave the hosts the lead before Nick Powell's equaliser, but Ismaïla Sarr secured all three posts for Watford, slotting the ball home at the death.
Victory sees Watford rise to 4th in the standings, while Stoke drop a place to 11th.
Story of the game
The hosts made just one change heading into the match, with Vladimir Ivić bringing in Christian Kabasele to replace William Troost-Ekong at centre-back. The main talking point for Watford was the inclusion of captain Troy Deeney on the bench.
Opponents Stoke fielded the same starting 11 that beat Rotherham United in their previous match, manager Michael O'Neill clearly showing a good degree of faith in those players.
It was a positive start from the visitors, with early pressure allowing James McClean the time and space to loft a cross in their area, but Kabasele was there to head away dominantly.
They had their lead in just a matter of moments though, as a well-worked short corner routine saw Powell cross for Steven Fletcher to prod home from a couple of yards out, capitalising from a sluggish and tentative beginning to the game for Watford.
The game was for the taking of the Hornets from this point on — out of possession, their opponents would sit deep and protect their lead, so could the hosts summon the quality within their ranks to get back on level terms and later take the advantage?
It was proving a difficult task — club-record signing Sarr let out a shriek of frustration when his misplaced pass fell to the feet of Morgan Fox, who in turn cannoned the ball off the Senegalese international and out for a Stoke throw.
Sarr and Kiko Femenía time and time again linked up well on Watford's right flank, but struggled to find the head of a teammate with their crosses which always seemed destined for the towering Danny Batth or centre-back partner Harry Souttar.
And Stoke could've had two 20 minutes in when full-back Tommy Smith bombed down the wing and supplied an early cross for the goalscorer Fletcher, but the 33-year old couldn't adjust his feet in time to trouble Ben Foster in goal.
But it was Watford that scored next. Sarr exchanged a superb one-two with Nathaniel Chalobah down the left and supplied a good cross for Cleverley. The captain for the night struck a vicious effort towards goal which Angus Gunn managed to fingertip onto the bar, and Pedro bundled the ball — and goalkeeper — just over the line in the subsequent scramble.
There was some controversy about this goal, as the Stoke players and staff believed Pedro had fouled Gunn to score the goal, but referee Andy Davies was unmoved.
Watford could've taken the lead moment later, capitalising on a lapse of concentration from their opponents to unleash Sarr through on goal, but the forward hesitated and gave the defence enough time to recover and block the resultant shot.
Chalobah then went close with a curling effort from the edge of the area. The Hornets were well and truly in the ascendency, and they began knocking the ball about with the confidence and swagger befitting of a team frequently tipped to challenge for the Championship title this season.
There was a lengthy pause to proceedings as Fletcher received treatment for a knock, but Watford's rhythm went uninterrupted. Femenía, their liveliest player in the first half, kept finding space behind Fox on the wing and supplied a sumptuous cross for Sarr on the stroke of half-time, but it was just too high for the 22-year old.
The Hornets started the second half as they ended the first: taking the initiative and searching to gain the lead. In the first few moments, Cleverley clipped a good ball in for Ken Sema who was just beaten to the header by Souttar, and Sarr then darted into the box but found the ball caught under his feet and the danger cleared.
But it was the Potters who came closest to scoring next when Tyrese Campbell's searching cross found the head of Powell. The former Manchester United man rose highest and had Foster stranded from about 10 yards from goal, but failed to direct his effort on target.
Not long after, a similar manoeuvre saw Smith given the space to loft a ball in from the right, and Fletcher was lurking ready to power home but for a crucial intervention from Kabasele.
Watford had survived a period of considerable pressure from their visitors, and they were rewarded with an excellent opportunity to take the lead for themselves when Sarr was fouled by Gunn in the penalty box.
Pedro duly converted to make it 2-1, his final touch of the match as he was immediately replaced by Andre Gray. And it was so nearly an instant impact from the forward as he saw his glancing header sailed just wide of the post on 72 minutes.
Stoke's defence didn't seem to enjoy having a fresh pair of legs to play against, but they coped and still managed to provide a solid base for attacks to be built from — and they knew they'd done just that when Powell powered home to equalise on 81 minutes, against the run of play.
The 26-year could have regained the advantage for his just moments later when Campbell teed him up on the edge of the area, but his effort was miscued and sailed way over the bar.
Tense would best describe the atmosphere in the closing stages as both sides looked to sneak the win without risking defeat. But Watford rose to the task and earned that crucial third and final goal.
Full credit should go to Sema, who wriggled past two challenges to get to and across the byline, before cutting the ball back for Sarr to slot home. It wasn't the final action in a dramatic end to the match as Batth's header forced Foster into a late save, but Watford got over the line in the end to secure victory after three games without it.
Takeaways from the match
Watford reminded they're here to compete, not conquer
The Hornets had taken just two points from their three games prior this, the realisation dawning that the Championship is an uncomfortable place to be after relegation from the Premier League. That should be ever more apparent to them now.
They huffed and they puffed hard enough to get another point here tonight, but it was another really difficult encounter and an indication that, despite the quality in their ranks, there is no guarantee whatsoever that Watford will linger in the upper echelons of the standings this season — they'll have to work hard for that.
Stoke can challenge for playoffs
In the first half particularly, the Potters looked positive and entirely unfazed by their opponents — and why should they be? There's potency and pedigree about their spine, including Souttar, Jon Obi Mikel, Powell and Fletcher who all performed impressively here in a game of very fine margins.
They weathered the storm from their opponents well and deserved their equaliser when it came; defeat was harsh. With O'Neill at the helm, Stoke will feel they have a good chance of challenging for one of those top six spots this season and possibly reclaiming their spot in the top flight having been absent since relegation in 2018.
Ismaïla Sarr (Watford)
His club valued him at around £35m in the summer of 2019, and Sarr went some way towards explaining why tonight with an effervescent and match-defining performance.
A thorn in the Stoke defence all game long, the forward won the penalty from which Pedro gave Watford the lead and went on to win the game for his side with a cool finish in the 93rd minute.
Keep him fit and firing, and the Hornets have a real weapon at their disposal.
Watford: Foster; Cathcart, Kabasele, Wilmot; Femenía, Cleverley (Garner 62'), Chalobah (Hughes 89'), Capoue, Sema; Sarr, Pedro (Gray 62').
Subs not used: Bachmann, Ngakia, Troost-Ekong, Deeney.
Stoke City: Gunn; Smith (Vokes 74'), Souttar, Batth, Fox; Obi Mikel, Thompson; Campbell, Powell (Cousins 85'), McClean; Fletcher (Brown 66').
Subs not used: Nna Noukeu, Lindsay, Tymon, Oakley-Boothe.
Watford return to Vicarage Road to host newly promoted side Coventry City at the weekend.
Meanwhile, Stoke travel to league-leaders Reading in what looks set to be an intriguing tie.