The Clarets put five players in midfield, ably led former Hornet Micah Hyde, and managed to control much of the game.
Watford were fresh from an impressive 3-0 victory over QPR in midweek and Ray Lewington's side never really threatened apart from a late, half-hearted flurry at the end.
Burnley had the better chances in the first half, even though the home side enjoyed the edge on play. Robbie Blake and Frank Sinclair both headed wide from crosses by the inventive Tony Grant.
Watford for all their possession struggled to test the Burnley keeper and lacked penetration in the first half.
After the break Paul Mayo forced Danny Coyne into a save when he hit a well taken free-kick and then a Heidar Helguson came on late to send a headed chance over the bar.
Watford's defence began to creak but when Robbie Blake picked out Richard Chaplow he shot wide.
But, after 65 minutes Burnley scored the winner. Keeper Richard Lee made a heroic attempt to deny them with a superb save, beating away a shot from Blake, but when the ball dropped into the path of Ian Moore he was left with a simple header.
Watford attempted to get behind the Burnley defence and Hameur Bouazza got free on the left, but his shot hit the side netting, while at the other end Blake saw his header brilliantly flicked away by Lee.
Mayo nodded over and Helguson sent an angled shot clear of the target to sound a death knell to Watford's hopes of retrieving a point.