A woeful first half started as it meant to go on with both teams scrapping over possession but failing to make any headway towards goals.
Chances were few and far between with Dave Brammer found room for a shot on 13 minutes that the midfielder scuffed wide off Alec Chamberlain's right post.
A heavy collision between Kenwyne Jones and Gavin Mahon forced the Watford man to leave the pitch and be replaced by Alhassan Bangura.
The Hornets' best efforts of the half came seconds before the break when Dominic Blizzard hit a 20-yard looping shot that Steve Simonsen had to tip over.
An improved second half produced a goal only six minutes when Hameur Bouazza climbed above the Stoke defence to head down for Heidar Helguson to finish from close range.
The addition of youngster Martin Paterson for the less than interested Jones gave the Potters attack a much needed shot in the arm.
Chris Greenacre gained space from Danny Cullip in the 65th minute to cross for an unmarked Brammer, however, his powerful header fell straight into the arms of Chamberlain.
Greenacre was in the thick of the action again soon after, this time creating something out of nothing when he hooked a shot from 20 yards on to the crossbar.
A determined Watford side dug in and broke the City pressure by retaining the ball late on to claim a place in the division for another year.