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.
The former Ipswich man's strike was one of just a few noteworthy incidents, with quality in short supply.
Large parts of the game were spent with both sides trading long balls and, short of a handful of effort from just inside the area, Watford rarely looked like recovering from their early setback.
There was no place in Leeds' starting line-up for new signing Ross McCormack, with Simon Grayson opting to select the same side that beat Millwall last weekend, and it reaped instant rewards as United took an early lead.
Scott Loach tipped Luciano Becchio's header over the bar but, after the home side failed to deal with the subsequent corner and crosses into the box, Naylor was on hand to tap in from close range after Troy Deeney allowed Bradley Johnson and Becchio to get the better of him.
With Watford missing four-goal Danny Graham to injury, Deeney was given a first league start in attack, and some good play from him allowed the Hornets to create a chance for John Eustace - but the skipper only able to fire wildly over the bar.
Deeney's striker partner Marvin Sordell then put an opportunity wide, as did Sanchez Watt at the other end, while Naylor had to earn his money in front of his own goal as he blocked a low drive from Stephen McGinn.
Leeds lost Fede Bessone to injury at the break and replaced him with Andy Hughes, but there was little for him and his fellow defenders, or the Watford back four, to do throughout the second period.
Jordan Mutch drilled wide for Watford and Becchio nearly got on the end of an arrowed cross from Johnson, and not even the introduction of Scotland winger McCormack could liven things up.
The winger, signed from Cardiff yesterday, did bring a save out of Loach with a deflected effort, but Leeds were rarely threatened and, on the rare occasions Watford did advance forward, Kasper Schmeichel's precision handling kept them at bay.