Goals from Dean Bowditch, James O'Connor and substitute Jean Louis Valois were enough, with Watford's consolation coming from substitute Dominic Blizzard.
Burnley were good value for their victory, although Watford, very poor in the first half, did show a lot of spirit later on and might easily have got themselves back on level pegging.
On-loan Ipswich striker Bowditch showed great composure to put Burnley ahead and Mo Camara had an effort disallowed before O'Connor's fierce shot gave Burnley a two-goal cushion.
Watford, under the new management of Adrian Boothroyd, were a different animal after the break, and it was no surprise when substitute Blizzard headed them back in the picture from a right-wing corner from Jermaine Darlington.
Ashley Young had a couple of long-range efforts flash high and wide as the visitors went in search of an equaliser and Burnley were forced to make defensive substitutions in an effort to hold on to their lead.
But unselfish play by the tireless Ade Akinbiyi finally settled matters in stoppage time. Akinbiyi won possession out on the right before rolling the ball across for the unmarked Valois to score with ease.
Watford, now without a win in seven, are just two points from the drop zone while Burnley wallow in mid-table security.