Sandwiched between both legs of a Champions League quarter-final with Bayern Munich, this Villa match was always going to prove a test for Arsenal and it was one they failed.
Kai Havertz forced Emiliano Martinez into a low save early on before both Gabriel Jesus and Bukayo Saka saw efforts hit the side-netting.
Gabriel Magalhaes has been a rock at the back for Arsenal this season but he gifted possession to Watkins, who almost took full advantage only to see his shot come back off the inside of the post.
Arsenal went straight down the other end and almost took the lead themselves only for ex-Gunner Martinez to make a stunning reflex save to keep out a close-range Leandro Trossard attempt.
Saka then curled a shot inches wide as Arsenal could not find a way through to relieve some of the pressure building around the Emirates.
The sides went in level at the break but Villa were the much better outfit after the interval, restricting the hosts to just four shots in the second half.
With his side in the ascendancy, Emery turned to his bench and introduced Bailey in place of Moussa Diaby, although it was Youri Tielemans who came close moments later.
Oleksandr Zinchenko was caught in possession on the edge of his own box, with Tielemans robbing the ball and hitting both crossbar and post with a fierce drive.
Arteta replaced Ben White, Martin Odegaard and Jesus as he looked to freshen things up but in the closing stages it was Champions League-chasing Villa who would push on to get the three points their performance thoroughly deserved.
