It was Stoke's third successive victory coming after a run of eight defeats and in Ade Akinbiyi they had the match-winner. The striker, ploughing a lone furrow up front, twice beat the Watford offside trap to find the net with low well-delivered shots.
Watford had taken the lead after just three minutes. A cross by Paul Devlin on the right was met by a tame header from Paulo Vernazza which was blocked on the line by a defender and the ball bounced straight to Heidar Helguson who slammed it home from six yards.
However, Watford's lead was wiped out after 15 minutes when Lenny Pidgeley, on loan from Chelsea for the season, failed to meet a John Eustace cross and Gerry Taggart met the ball to head firmly into the empty net with the keeper in no man's land.
Stoke continued to look the better side and Akinbiyi had a reasonable chance when Marcus Hall sent over a cross but the striker headed down and into the ground.
Watford rallied towards the end of the first half and from another Devlin cross the home skipper, Neil Cox, was presented with a good chance but he sent his header straight at keeper Ed de Goey.
But Akinbiyi sounded a warning when he turned well on a pass from Clive Clarke and it took a timely block by Pidgeley to clear the danger.
Watford had what looked like a good appeal for a penalty turned down just before the interval when John Halls pushed Helguson in the box as the keeper collected a cross.
The referee waved play on. Pidgeley was again in the action early in the second half pulling down a shot on the turn from former home striker Gifton Noel-Williams.
City took the lead slightly against the run of play as Watford created some nice moves down the left with the introduction of winger Lee Cook.
But Stoke broke well with Darel Russell sending the ball through for Akinbiyi to home in on the hesitating Pidgeley and strike an angled shot low into the net.
Scott Fitzgerald fired straight at the keeper and Helguson headed wide as Watford looked for an equaliser.
Ray Lewington introduced two substitutes but they failed to make much impression on a determined Stoke rearguard that had their tails up after 72 minutes when City increased the lead.
Again Watford were looking in vain for the offside flag as Clarke released Akinbiyi who homed in on goal to shoot low pass the keeper.
Watford were unable to match such clinical finishing - Bruce Dyer fired wide on the turn and Cook, after breaking into the City penalty area, saw his goalbound shot blocked by De Goey's outstretched leg.
Akinbiyi fired wide in a bid for his hat-trick but the only disappointment for City was the dismissal of Halls two minutes from time.
He reacted angrily to a challenge from Helguson who was booked while the City man was shown the red card.