Raheem Sterling’s goal in the first half was enough to secure the three points for Pep Guardiola’s side.
Aubameyang, meanwhile, struggled to make an impact on the left flank as Arsenal found it difficult to create clear-cut chances.
Shortly after the final whistle, Aubameyang shared a brief exchange with his former Borussia Dortmund teammate.
But Arsenal supporters were unhappy at the sight of Aubameyang smiling so soon after the Gunners were beaten.
Arsenal fans made their frustrations clear on social media, with one posting on Twitter: ‘Why the f*** is he so happy. We just lost with an abysmal display with almost no players actually being asked to do anything.’
Another Arsenal fan added: Surely could have waited till he was down the tunnel at least. I don’t care what he does just a time and a place to be having a laugh.’
One supporter said: ‘Laughing after a loss… he’s captain.’
While another Arsenal fan wrote: ‘Auba standing chatting and having a laugh with a city player after a defeat is simply not acceptable.’
Other Arsenal supporters pointed out that Mesut Ozil, who was left out of Mikel Arteta’s matchday squad once again, would have received far harsher treatment from fans if he had the same reaction after the final whistle.
Arsenal will then host Leicester City in the Premier League next Sunday.