Darren Fletcher volleyed his first goal for Stoke to take the wind out of Watford's sails.
The Hornets were looking to cement their place in the top six, but Fletcher's Paul Scholes-style strike from the edge of the area secured a first away win for City.
The 1-0 victory also eased the pressure on Stoke manager Mark Hughes, who was in danger of becoming the latest boss under the microscope following four defeats in five matches.
Yet Watford had started with all the confidence of a team who kicked off in sixth place in the Premier League, with wingers Andre Carrillo and the in-form Richarlison looking in particularly menacing mood.
But for all their swagger in the first 15 minutes, they could not find a way past the massed ranks at the back for Stoke.
Instead, with their first corner of the match, the visitors took the lead courtesy of Fletcher.
The strike was reminiscent of one his old Manchester United team-mate Scholes might have scored, as the midfielder met Xherdan Shaqiri's cross with a crisp volley from the edge of the area.
The ball may have taken a slight deflection on its way underneath Hornets goalkeeper Heurelho Gomes, but Fletcher did not care as he raced to celebrate with Hughes on the touchline.
The closest Watford came to equalising before half-time was also from a corner, Miguel Britos heading a Jose Holebas cross narrowly wide.
They came closer still shortly after the interval when Carrillo headed another Holebas delivery back across goal from where Richarlison fired into the side-netting.
Stoke had their moments early in the second half, not least when Ramadan Sobhi raced to the byline and cut back for Joe Allen, who dragged his shot wide.
But Watford piled forward and Richarlison, who was guilty of two bad misses in the 4-2 defeat at Chelsea last weekend, blew another chance by nodding a Britos cross wide at the far post.
Potters substitute Saido Berahino should have wrapped things up six minutes from time when he raced through but prodded his shot wide to prolong his search for a Stoke goal.
Tempers then momentarily flared and Abdoulaye Doucoure and Mame Biram Diouf were booked after squaring up on the touchline, and another melee in injury-time saw Allen and Troy Deeney go into the book.
Seconds later Charlie Adam thought he had settled the match when he skipped past Gomes, who had gone up for a corner, but when he rolled the ball towards an empty net it came back off a post.
Nevertheless Hughes and Stoke had done enough to earn themselves some respite at the foot of the table.