Headers from Jeff Hendrick and Michael Keane handed the Clarets all three points against Walter Mazzarri's side, who failed in their attempt to win three Premier League games in a row for just the second time ever.
The home side went into the match as the lowest-scoring team in the Premier League so far this season, but it was they who made the brighter start to proceedings in search of their first win in five games.
Despite their early dominance in what was the first top flight meeting between the two sides, Burnley were forced to settle for half-chances for the most part as a couple of Sam Vokes headers failed to trouble Heurelho Gomes in the Watford goal.
Gomes was called into action once in the opening exchanges, though, and he needed to be alert to tip George Boyd's quick snapshot over the crossbar after Watford had failed to clear their lines from a corner.
Sean Dyche watched his side continue to get the better of his former club - where he spent more than a year as manager following spells as player, youth coach and assistant - and summer signing Johann Berg Gudmundsson almost turned their dominance into a lead midway through the half when he cut inside before firing a low effort narrowly wide.
Watford finally had their first sight of goal after 26 minutes when a corner was floated directly to Jose Holebas on the edge of the box, but the full-back's first-time volley was cleared before it could trouble Tom Heaton.
The first half showed few signs of the Hornets ending an eight-match, 12-year wait for victory at Turf Moor, and that ambition slipped further away when Burnley took the lead with just seven minutes remaining before the interval.
The opener came via a corner as Steven Defour floated the ball into the box for Hendrick, making his home debut for the club, to nod into the bottom corner for his first ever Premier League goal.
One almost became two moments later as Burnley again threatened from a set piece, but this time Vokes could not apply the finishing touch to Ben Mee's knockdown.
It wasn't until first-half stoppage time that Heaton had to make his first save - a comfortable one from Odion Ighalo's header - but he was finally called into serious action early in the second half when he kept out Troy Deeney's powerful strike with a smart stop at the near post.
The visitors had made a brighter start to the second half, but they were soon stopped in their tracks as Burnley doubled their advantage five minutes after the restart, with Keane also opening his Premier League account by glancing Defour's cross into the bottom corner.
Burnley could have killed the game off once and for all shortly after the hour mark when Gomes parried Defour's powerful strike into a dangerous area, but Vokes and Mee got in each other's way in their attempts to turn the rebound home.
Moments later Watford created a rare chance at the other end as the game began to open up, but Deeney could not get the required power on his header across goal to trouble Heaton.
It was Burnley who almost sealed the victory in the final 10 minutes, though, as a lucky bounce saw the ball break into the path of Boyd, who seemed to be caught in two minds with Hendrick in the middle and subsequently failed to make the most of a promising position.
The clock was against the visitors, though, and despite four minutes of added time they failed to find a route back into the match as Burnley safely saw out the victory to make it three home games in a row without defeat in the top flight.
The Clarets move up to 13th in the Premier League table as a result of the victory, now level on points with Watford, who remain 11th. body check tags ::