Per Mertesacker had given Arsenal the lead on his first top-flight start in 18 months, but a penalty from Troy Deeney and Tom Cleverley's last-gasp winner - the third successive game in which Watford had scored in added-on time - earned the Hornets their first home win over the Gunners since 1987.
Arsene Wenger will argue that Watford should not have been awarded a spot kick with Richarlison appearing to fall to the ground too easily, but the visitors did not take their chances and suffered their first defeat in eight games in all competitions.
Both teams went into the game at Vicarage Road after a positive run of form, but their attacking play left a lot to be desired during a drab opening to the match.
Arsenal needed almost half-an-hour to get their first strike on goal, with Mohamed Elneny taking the chance to move forward before firing a 25-yard strike marginally over the crossbar.
However, from that moment onwards, the Gunners began to have more joy in the final third and with six minutes of the half remaining, the North Londoners went in front.
Granit Xhaka's corner found Mertesacker all on his own on the edge of the six-yard area, and the centre-back did not need to be asked twice to score his first Premier League goal in nearly four years.
Watford improved after the restart with Richarlison heading numerous attacks for the home side, but the summer signing was unable to get his team back on level terms with a curling effort from just inside the box.
Just before the hour mark, Arsenal's Danny Welbeck was forced off with another injury but his replacement - Mesut Ozil - was soon orchestrating the play, with a through-ball finding Alex Iwobi who was superbly denied by Gomes.
Ozil should have then doubled Arsenal's lead after finding himself in time and space inside the penalty area but the playmaker placed his shot far too close to Gomes, who guessed correctly in diving to his left.
Less than a minute later, Watford had a penalty. Bellerin has harshly adjudged to have pushed Richarlison inside the penalty area and Deeney made no mistake from 12 yards as he sent Petr Cech the wrong way for his first league goal in 14 matches.
The momentum was with the home side and with less than 10 minutes to go, Etienne Capoue came agonisingly close to completing the turnaround when his shot deflected off Mertesacker and struck the outside of the post.
However, in the second minute of added-on time, Watford won it through Cleverley, who was perfectly placed to fire the ball into the roof of the net after two blocks from goalbound efforts.
Arsenal attempted to rally but Watford survived, leaving the Gunners nine points adrift of leaders Manchester City after a third setback of the season.