The Hornets fell to their first home defeat since the end of August as Stoke City claimed all three points on Sunday afternoon.
Charlie Adam’s header deflected in off the post and then Heurelho Gomes, and it proved to be the winner in what was otherwise a close affair in the Premier League.
A frustrating afternoon was made worse for the hosts as Miguel Britos was sent off for a second yellow card in the last minute of normal time.
Walter Mazzarri made one change to his starting XI for the visit of Mark Hughes’ Potters.
Jose Holebas returned to the side and replaced Camilo Zúñiga on the left-flank for the Hornets, as they looked to build on last weekend’s impressive victory against Leicester.
The visitors fashioned the first clear-cut chance of the game as Gomes was forced into two smart saves following a dangerous ball whipped into the box by Xherdan Shaqiri.
Moments later and Daryl Janmaat broke quickly through the middle of the pitch but the full-back’s low strike at goal was well held by Lee Grant in goal for the Potters.
With a quarter-of-an-hour gone Giannelli Imbula broke at goal before unleashing a powerful drive which flew narrowly wide of Gomes’ goal.
The Hornets responded through Etienne Capoue, who too tried his luck from distance following a lay-off from Nordin Amrabat. The midfielder’s powerful strike was well saved by Grant though as he collected at the second attempt.
Mazzarri was forced into his first change of the afternoon as Younes Kaboul came off injured just 20 minutes in. The central defender was replaced by Christian Kabasele.
Midway through the half Roberto Pereyra turned his way towards goal on the left-flank before opening his body and curling an effort towards goal. It was in a similar position to his spectacular strike against Leicester last weekend, but this time it flew wide.
Just before the half-hour mark the Potters took the lead in slightly fortuitous fashion. Shaqiri whipped a corner into the box which Charlie Adam met with a header. His effort bounced off the post and deflected in off Gomes, who had dived across in an attempt to knock the ball wide.
The Hornets created chances to get back into the game as Capoue’s free-kick from the right was headed over by a combination of Britos and Sebastian Prödl.
With minutes left in first-half added time, Glen Johnson appeared to bring down Holebas as he broke into the box, however replays proved that the defender had timed his challenge perfectly.
A minute into the second-half, the Potters were nearly two goals up. Marko Arnautović broke with pace and his ball across the box narrowly missed the on-rushing Jonathan Walters, who had burst into the box.
Mazzarri made his second change of the afternoon 10 minutes into the second-half, with Holebas replaced by Odion Ighalo as the Hornets went in search of an equaliser.
Soon after, Walters got onto the end of Erik Pieters’ free-kick into the box but the midfielder put his header over the bar.
With just over 10 minutes left to play the Hornets made their third and final change of the afternoon as Amrabat was replaced by Stefano Okaka up top.
The Hornets poured forward and Pereyra’s ball into the box fell to Janmaat outside the area, but the full-back’s volley at goal sailed wide of the target.
It was the hosts who were creating the better of the chances as the game neared an end with Ighaho’s attempted over-head kick falling to Okaka. The striker’s shot from the tightest of angles however failed to test Grant.
Deeney too went close as he got in front of his man to meet Janmaat’s lofted ball into the area, but his headed effort went over the bar.
With a minute left of normal time the Hornets were reduced to 10 men as Britos was shown a second yellow card. Shaqiri broke from a corner but was tugged back by the defender as he made his way into the Watford half.
The full-time whistle followed to bring to an end what was a disappointing defeat at Vicarage Road. The Hornets will now turn their attentions to West Brom as they look to bounce back next Saturday.
HORNETS: Gomes (GK); Kaboul (Kabasele, 19), Prödl, Britos; Janmaat, Capoue, Behrami, Holebas (Ighalo, 55); Amrabat (Okaka, 78), Deeney (c), Pereyra.
Subs not used: Pantilimon (GK), Mariappa, Zuniga, Guedioura.
Yellow cards: Amrabat (24), Britos (26), Holebas (40), Britos (90), Behrami (90)
Red card: Britos (90)
POTTERS: Grant (GK); Johnson, Muniesa, Martins Indi, Pieters; Adam, Imbula; Walters (c), Shaqiri, Arnautovic (Crouch, 81); Diouf.
Subs not used: Given (GK), Bony, Bojan, Sobhi, Ngoy, Verlinden.
Goal: Gomes OG (29)
Referee: Bobby Madley