The Clarets had not won in their previous four games and were on course for defeat when Martin Taylor headed home in the 57th minute to put Watford 2-1 up.
Yet Brian Laws' men roused themselves and drew level through substitute Ross Wallace in the 70th minute before Graham Alexander hit the winner from the penalty spot with 13 minutes remaining.
Burnley went close inside the opening three minutes when Tyrone Mears crossed dangerously and Jay Rodriguez headed just wide from 12 yards.
They threatened again in the 10th minute when Wade Elliott collected possession 18 yards from goal and hit a shot just wide of the mark.
In the 12th minute Taylor fouled Rodriguez and Jack Cork's free-kick found its way to Chris Eagles.
The former Manchester United trainee hit a shot from 25 yards which drew a fine save from Hornets goalkeeper Scott Loach.
Cork, on loan at Turf Moor from Chelsea, then fired over from 25 yards and in the 19th minute the Clarets went close again.
An outswinging corner from the right flank by Graham Alexander was greeted by a firm header from Michael Duff but his effort flew wide of the mark.
In the 25th minute, Burnley opened the scoring as Chris Iwelumo latched onto Rodriguez's flick and headed the ball past Loach from 12 yards.
Yet the response from Watford was admirable and they almost drew level in the 29th minute when Don Cowie shot just wide from six yards.
Less than a minute later the equaliser did come when Cowie found the space to hit a left-footed shot into the net from bottom right-hand corner from 12 yards.
Iwelumo then mishit a shot from 12 yards when he should have done better and Eagles shot over from 20 yards as the sides went in at the break all-square.
Four minutes after the restart, Cork headed over the crossbar as Burley sought to regain the lead.
However, Watford continued to pose a threat and they forged ahead in the 57th minute when Taylor rose to connect with Jordon Mutch's cross and plant a firm header into the net.
Clarets boss Brian Laws then made a double substitution in the 66th minute, replacing Elliott and Iwelumo with Wallace and Steve Thompson.
And the switch paid dividends as Burnley drew level in the 70th minute when Eagles crossed dangerously and Wallace arrived to fire a left-footed shot into the net from six yards.
The Clarets continued to probe and claimed the winner in the 77th minute when Taylor fouled Rodriguez and Alexander kept his cool to fire home into the top corner from the penalty spot.