The substitute had been on the pitch just 104 seconds when he broke the deadlock in the 77th minute, collecting Chris Iwelumo's knock-down and seeing his initial sloppy effort blocked by goalkeeper Steve Harper before following up to convert the rebound.
It was a deserved victory for the Hornets based on their dominant first-half display, in which Harper was in fine form and Adrian Mariappa headed against a post.
The Seagulls stepped up a gear in what was a low-key second period but still failed to register a single shot on target as their winless sequence stretched to nine successive league matches, with the south-coast outfit having failed to score in four of their last five.
It was only a third win of the season for Sean Dyche's lowly Watford, who have opened up a four-point gap over third-bottom Coventry.
For the second successive match Brighton sustained injury in the pre-match warm-up, right-back Gonzalo Jara Reyes the man to make way with Ryan Harley coming into midfield.
Billy Paynter was also handed his full debut after last week's loan move from Leeds.
Watford, meanwhile, remained unchanged following their 3-2 victory over Peterborough.
And it was the hosts who made a blistering start to proceedings.
Mark Yeates saw his shot well saved by Brighton goalkeeper Harper with just a minute on the clock before Prince Buaben fired the rebound wide.
Harper was quickly called into action soon after to turn Marvin Sordell's angled shot around a post.
Craig Forsyth was next to test the on-loan Newcastle stopper before Mariappa, wearing the captain's armband in the absence of the injured John Eustace, sent a header against the foot of a post from Yeates' free-kick.
Watford were reminded of the visitors' threat when Craig Noone fired narrowly wide of the upright following some sloppy defending from the hosts.
Brighton boss Gus Poyet was forced into another unwanted change after 30 minutes when he lost Liam Bridcutt to injury, with player/assistant manger Mauricio Taricco coming on to replace him.
The early excitement subsided somewhat as the first half wore on but Sordell did twice go close for the Hornets, with a header and half-volley both flying off target.
As they did in Saturday's goalless draw at Birmingham, the Seagulls improved in the second half as they started to spread the ball around.
Watford were struggling to impose themselves in the same manner as they did in the first half and manager Dyche introduced on-loan Wolves winger Michael Kightly from the bench on the hour mark.
The majority of the 11,818 inside Vicarage Road saw an appeal for handball waved away.
At the other end, Gordon Greer's flick-on found the side-netting but there was considerably less action after the restart.
That was until Deeney proved his worth within two minutes of stepping off the bench.
The former Walsall man was denied a second by a good block from substitute Ashley Barnes, but it was he who remained the matchwinner come the final whistle.