BURNLEY ended the first half on the front foot after responding to going behind in the 10th minute.
Charlie Austin cancelled out Nathaniel Chalobah's 18-yard strike from the penalty spot, after Joel Ekstrand pushed Dean Marney in the box.
Austin was asked to replace the ball on the spot, while Manuel Almunia was booked for trying to delay the penalty further.
But the top scorer held his nerve to send Almunia the wrong way and slot his in his 22nd goal of the season.
David Edgar had been denied seconds early.
The Canadian had been involved in the build-up to Watford's opener after he suffered a clash of heads with Alex Geijo in trying to deal with a ball into the box, it dropped for Chalobah on the edge and he managed to beat Lee Grant at his near post with a speculative volley.
Edgar recovered quickly, and got on the end of an excellent Ross Wallace free kick two yards out, but was denied by former Arsenal goalkeeper Almunia.
The Clarets grew in confidence and could have gone ahead with further chances for Austin, Martin Paterson and Danny Ings, in his first start of the season following a serious summer knee injury.
Watford still posed a threat, but Burnley ended the half with more possession and the better of the chances.