Suspensions and injuries meant the Hornets had to make three changes from the 2-0 win at Norwich ahead of the international break, while the visitors were unchanged from their 3-0 victory over West Ham.
The game started in a scrappy manner with neither side able to take control but as the match went on, the hosts started to gain the upper hand.
Gerard Deulofeu had their first real chance, dispossessing James Tarkowski before striding forward. Breaking towards the box, the Spaniard unleashed an effort which forced Nick Pope into a smart save.
Deulofeu also tested the England goalkeeper with a free-kick in first-half stoppage time, five minutes of which had been awarded after a break in play when Craig Dawson was forced off with a head injury.
The second half continued to be a scrappy affair but the deadlock was broken in the 53rd minute and it was a smart finish by Chris Wood, hooking the ball home from Tarkowski’s knockdown.
VAR had a look but the goal was clean; however, there will be controversy as Ben Mee had clearly fouled Adrian Mariappa as he cleared for the corner that produced the opener.
Troy Deeney came on soon after for the hosts but chances were few and far between, Jeff Hendrick forcing a save out of Ben Foster while at the other end, Pope was flawless.
Burnley’s best efforts were again on the counter-attack, substitute Jay Rodriguez latching onto a long ball and looping onto the bar.
The game was gone soon after, Jose Holebas fouling Ashley Barnes in the box with a penalty given. Paul Tierney let things run but VAR made the call and Barnes smashed in, albeit despite a valiant effort by Foster.
It was left to Tarkowski to finish the scoring, finding space from a free-kick and, after seeing his first effort saved, drove home with his left foot.
Deulofeu did hit the bar in stoppage time but it was too little too late for a Watford side who, with the teams around them picking up points, have slipped to the bottom of the table.
Burnley, in contrast, are now up to sixth after breaking their away day duck.