Leeds' skipper Richard Naylor marked his 450th career appearance with the only goal as the the 33-year-old was in the right place at the right time after just six minutes to prod home the 45th goal of his career and keep Leeds' fine start to the campaign going.
And despite enjoying the majority of possession for much of the match, the Hornets were unable to find an equaliser.
Watford were without Danny Graham due to the striker picking up a groin injury shortly after coming on in Tuesday night's Carling Cup defeat to Notts County.
Martin Taylor, who made his 250th professional start today, captain John Eustace and Lee Hodson were all left out midweek but returned to the starting line-up.
Jordon Mutch, who was ineligible on Tuesday, made his first Watford start in place of Will Buckley, while Josh Walker also returned to the bench.
The Hornets had two free kicks in decent areas early on but both were easily cleared and they found themselves a goal behind within six minutes.
Scott Loach, who was back in the side after being rested, did well to tip over a Luciano Becchio header but there was little the keeper could do when Neil Kilkenny sent in the resulting corner.
Terrible marking wasn't punished as a Bradley Johnson header and Johnny Howson shot were blocked but when Marvin Sordell headed the ball aimlessly back into his six-yard box, Loach did well to get a hand to Becchio's close-range header and Naylor was able to tap home from close range.
Watford responded immediately and John Eustace, who was on the verge of signing for Leeds in the summer, should have tested Kasper Schmeichel when, unmarked, he sliced a volley wide from ten yards after a knock down from Taylor.
Watford looked shaky at the back though and Arsenal loanee Sanchez Watt was left unmarked to head a Lloyd Sam cross wide.
The Hornets were regularly not picking up their markers and for that reason, Leeds looked a threat whenever they went forward in the opening stages.
But the home side did create the better chances after the goal. Sordell had a shot saved at the near post after Deeney slid him through.
Deeney, who was making his first Championship start, chipped over the bar after some steady build-up from the Hornets.
And after poor marking saw another Leeds' header blocked, Sordell beat Schmeichel to a through ball but the keeper stopped his stab at goal.
Stephen McGinn had a goal-bound shot blocked and then the Scotland Under-21 international fired over after Eustace headed straight at Schmeichel from a Don Cowie corner.
Johnson had a deflected shot gathered by Loach but besides that, Leeds did not create another chance for the rest of half.
It was a similar pattern early in the second half as Mutch dragged a shot wide from 25 yards out.
Watford were struggling to find any rhythm and it took them until the 55th minute to create their next chance.
Deeney did well to generate power on his header from 15 yards out but it was never going to trouble Schmeichel. The keeper did well to hold on to a powerful strike from Mutch soon after though.
Schmeichel, son of legendary United keeper Peter, looked assured at the back and claimed a couple of dangerous crosses to relieve the pressure on his side.
Substitute Max Gradel had a shot blocked but Leeds continued to struggle to create anything of note.
There was a worrying moment for the Hornets on 70 minutes though when a cross wasn't cleared and Johnson's cross-shot at the far post bounced around the six-yard box before being smashed away.
Watford were still pushing for an equaliser though and Paul Connolly just headed the ball clear before Deeney arrived at the far post.
It was a very scrappy contest and Leeds almost grabbed an untidy second with 15 minutes remaining when Johnson's hopeful header into the box wasn't gathered by Loach and Mariappa just scrambled the ball clear in time.
Watford had a decent spell when a few of Cowie and Buckley crosses posed a few problems for Leeds, but on each occasion Schmeichel gathered or the ball was cleared.
The home side had a penalty appeal with two minutes of normal time remaining when Mutch did well to cross and Eustace's header was deflected into the arms of Schmeichel. The fans in the Rookery felt the ball had struck the arm of Collins but the referee did not award a spot kick.
Johnson sliced a shot wide of the near post in first-half injury time but the visitors rarely troubled the Watford goal.
And despite the Hornets using Taylor as an emergency striker, Schmeichel continued to claim any balls into the box as Leeds held on to their slender lead.
Watford starting XI: Loach; Hodson, Mariappa, Taylor, Doyley; Eustace, McGinn (Buckley 64), Cowie, Mutch; Sordell, Deeney.
Subs: Gilmartin, Bennett, Jenkins, Bryan, Walker, Henderson.
Leeds: Schmeichel; Connolly, Collins, Naylor, Bessone (Hughes 45); Sam (Gradel 60), Howson, Kilkenny, Johnson; Watt, Becchio.
Subs: Higgs, Bruce, Clayton, Somma, McCormack.
Attendance: 14,039 (2,199).
Referee: James Limmington.