Pierre-Emerick Aubameyang’s 84th minute free-kick completed the comeback for a vital three points after three league games without a win for Emery’s men.
“For me there are two things I will take from today. One is the character, spirit and connection with the supporters. And two, how we can improve defensively,” said Emery.
The Gunners’ defence was again exposed, even when with a full compliment of players, as Villa enjoyed the better of the first-half.
John McGinn was a constant threat as the Scottish international twice tested Bernd Leno from outside the box early on.
However, the hosts failed to heed those warning shots as McGinn was allowed to ghost in at the far post to turn home Anwar El Ghazi’s cross on 20 minutes.
Ainsley Maitland-Niles then naively dived into a sliding challenge with Neil Taylor four minutes before half-time and saw a second yellow.
The hosts were handed a lifeline just before the hour mark when Matteo Guendouzi was bundled over in the box by Bjorn Engels.
Emery confirmed Aubameyang was his designated penalty taker, but he stood aside to let Pepe net his first goal since joining Arsenal for a £72 million (HK$700 million) club-record move from Lille.
“It was a very big decision to let him shoot, to give him confidence,” said Emery. “The responsibility was Aubameyang’s. He’s hungry every day to score, to achieve individual marks, so that decision is one of a great player.”
Arsenal’s joy did not last long as their leaky defence was breached easily once more.
Jack Grealish galloped freely through the midfield before squaring for Wesley to prod in at the near post.
Tom Heaton held Arsenal at bay until the final 10 minutes as he turned Guendouzi’s long-range drive onto the post and tipped over David Luiz’s dipping free-kick.
However, Calum Chambers was in the right place nine minutes from time to score his first Arsenal goal since 2016.
In a topsy-turvy start to the season, Aubameyang has been the man Arsenal can rely on.
The Gabon international was fouled on the edge of the box six minutes from time and drilled his seventh goal of the season beyond the unsighted Heaton. (AFP)