Arsenal have lost four of their last five games in the Premier League to fall a long way behind north London rivals Tottenham Hotspur, who are in fourth spot.
Watford's Troy Deeney had a penalty saved three minutes later before Henrikh Mkhitaryan sealed the win on 77 minutes.
The Armenian playmaker played an inch-perfect pass to Aubameyang who raced clear of the Watford defence to double Arsenal's lead yesterday.
Victory over Watford took sixth-placed Arsenal to 48 points, but they are still eight points behind fifth-placed Chelsea in the race to secure Champions League football for next season.
Ray Parlour still doesn't expect Arsene Wenger to be at Arsenal next season.
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It was the Tricolors' first win over England in four years in the championship, and a welcome respite. An attack from deep saw a Jones chip and catch and Hogg inside him with only the posts ahead.
"It was very hard after a few defeats, but we could find the strength, power to play at home and to show that it was by accident that we lost three games in a row", Mkhitaryan said in a post-match interview with beIN Sport.
"It's quite fortunate that it's against Deeney", Wenger said, adding that his players had been keen to send a message to the striker.
And it seems the former Manchester United defender may well have been correct, considering Sunday's similar attendance; however, it did not stop him taking another swipe on Twitter at the Emirates Stadium regulars. We have shown spirit and we are in a strong position now against Milan.
Karnezis then denied Ozil as Arsenal pressed for a second goal but, with half-time approaching, back came Watford and Kiko Femenia's cross was diverted onto the roof of his own net by Rob Holding.
The home side made another change as the game headed for its final 15 minutes, Mustafi coming off to be replaced by Calum Chambers.
Watford play in the Premier League next Saturday with a trip to Liverpool (17:30 GMT).