Arsenal took the lead through a first-half header from Per Mertesacker, then Troy Deeney equalised for the Hornets before Tom Cleverley won the game in dramatic fashion in stoppage time.
The first half was a quiet affair, with chances at a premium. Both sides largely evened eachother out, as Watford had switched to back-three to match their opponents.
The Watford defence had to be on their toes to deal with a number of dangerous crosses from the Gunners but they defended well to stop any chances.
The first half-chance of the match fell to the Hornets. Abdoulaye Doucoure fired in a cross from the right, but it was too fast for Roberto Pereyra, who just about got his head to the ball but didn’t get enough contact and the ball went wide.
Mohamed Elneny came close to breaking the deadlock after 28 minutes when he let fly from 25 yards out, but his shot went inches over Heurelho Gomes’ crossbar.
Arsene Wenger’s side took the lead with the first effort on target of the match after 39 minutes. Per Mertesacker rose above Tom Cleverley to meet an inswinging corner from Granit Xhaka and powered his header past Gomes to make the breakthrough.
The Gunners seemed to step up after the goal and were close to doubling their lead, as Gomes got down well to save an effort from Xhaka following a cutback from Danny Welbeck.
Hector Bellerin was then presented with an excellent chance to double score his side’s second goal, but sliced wide from six yards when the goal was gaping.
Marco Silva’s side stepped up their performance in the second half and came out from the dressing room with more purpose.
Richarlison came close to equalising for the home side but his curling effort bent just wide of Petr Cech’s post after 52 minutes.
Despite the Hornets’ dominance, Arsenal were looking dangerous on the break, and Christian Kabasele made a vital block to stop Alex Iwobi running on to a pass from Alexandre Lacazette.
Mesut Ozil, who had just come on for the injured Danny Welbeck, was presented with a golden chance to double his side’s lead on the 70 minute mark. The German had a one-on-one with Gomes but couldn’t put the ball poas the Brazilian and the scores stayed at 1-0.
Moments later, Ozil would live to regret that vital miss. Richarlison powered past Bellerin on the left-hand side, and the Spanish full-back was adjudged to have brought the winger down by the byline.
The penalty decision looked soft as it appeared that Bellerin got a foot to the ball first, but nevertheless Watford skipper Troy Deeney, who had replaced Andre Gray earlier in the half, calmly dispatched the penalty to Cech’s left to make it 1-1 and score his first goal of the season.
After the equaliser it was the hosts who were in the ascendency and always looked like the side who were going to take all three points.
Richarlison smashed into the side netting from the left corner of the box and Deeney worked the ball back to Etienne Capoue, whose effort was deflected onto the post with Cech wrongfooted.
Watford got the goal which their positive play had deserved, scoring in stoppage time for the third league match in a row. There was mad scramble in the Arsenal box as Watford saw two shots blocked, but the ball eventually fell to Cleverley 10 yards out, and the midfielder smashed the ball into the roof of the net to win it for his side and score his first Watford goal since re-joining the side in January last season.
The Gunners suffered their first loss since the 4-0 humiliation at the hands of Liverpool in August, and sit in sixth place after the defeat, 9 points behind league leaders Manchester City.
Meanwhile, Marco Silva’s first home win since joining Watford in the summer, helped them move up to fourth place with 15 points after an excellent start to the season.