The Gabon star’s second-half double came either side of Bukayo Saka’s strike as the Gunners cruised to victory against the struggling visitors.
Mikel Arteta had Kieran Tierney back in his starting line-up after the Scot had missed last week’s draw with Crystal Palace as a precaution, while Thomas Partey was also included, having made his comeback from injury as a substitute against the Eagles.
Aubameyang missed the best chance of the first half when he guided Saka’s low strike back across goal and off the far post with the net gaping, but the Arsenal captain would make amends after the restart when he was sent away down the left by Partey and lashed a smart finish past Karl Darlow.
Saka doubled the lead just after the hour mark after superb work from Emile Smith Rowe, whose low pull-back was swept home to all-but end the game as a contest.
Alexandre Lacazette was denied by Darlow after being picked out by Saka, but Aubameyang soon added some gloss to the scoreline as he sidefooted his second after Cedric Soares had just about prevented the ball from going out of play to cross for his skipper.
The result means Steve Bruce’s side have now gone nine games without a win in all competitions, while Arsenal have kept five successive clean sheets as their upturn in form continues.