Danny Graham struck either side of a goal from Henri Lansbury before substitute Marvin Sordell put the seal on an easy win for Malky Mackay's men.
Watford suffered a 3-2 home defeat to Chris Coleman's men back in September, but this latest success means they have now won six of their last seven games against the Sky Blues.
But Coventry have seen their season fizzle out in recent weeks and this final-day defeat stretched their winless run to 11 games.
The hosts could have been in front after just nine minutes had Aron Gunnarsson not wastefully headed over the bar from Martin Cranie's cross.
But that miss proved costly as Graham, who joined the Hornets last summer, placed his 16th-minute penalty beyond Keiren Westwood after being fouled by Cranie in the box.
The Hornets doubled their advantage just a minute later when youngster Michael Bryan, who was making his first ever start for the club, set up Arsenal loanee Lansbury to unleash an unstoppable low strike from 30 yards.
Watford wasted the chance to add a third soon after as Lansbury's weak effort failed to trouble Westwood in the Coventry goal.
Coventry tried to claw themselves back into the game but Clinton Morrison saw his effort blocked by Adrian Mariappa before David Bell shot wide of the left-hand post.
The Sky Blues continued to push forward, but were having no luck in front of goal as several efforts were blocked by the Watford defence, while Freddy Eastwood and Morrison both failed to hit the target.
But, despite all their chances, Coventry almost fell further behind as Lansbury's left-footed strike was parried by Westwood before captain John Eustace shot wide of the mark against his former club.
Coventry were again cursing their luck when they were forced into a change at half-time, with Sammy Clingan going off to be replaced by Carl Baker.
But that did not deter Coleman's men from pushing forward in search of a goal in the early stages of the second half as Morrison shot wide of the right-hand post and substitute Baker saw his effort blocked by Lee Hodson.
Watford almost increased their advantage with their first noteworthy effort of the half after 56 minutes. Don Cowie latched onto Jon Harley's cross before firing an effort goalwards but, luckily for the hosts, Westwood was on hand to tip the shot round a post.
The Hornets finally added a third 12 minutes from time as Harley set up Graham to net his 14th goal of the season. Sordell then scored the fourth three minutes later when he fired a right-footed shot into the bottom corner from 12 yards.