After a goalless first half in which Arsenal failed to click into gear, Aubameyang gave the Gunners the lead from the penalty spot in the 75th minute at The Emirates.
The January signing from Borussia Dortmund then added a second goal to make it 2-0 in the 86th minute with a cool finish.
And substitute Alexandre Lacazette then netted Arsenal’s second penalty of the afternoon to notch up all three points for the Gunners.
Arsenal’s main focus will be on Thursday night, when they host CSKA Moscow in the first leg of their crunch Europa League quarter-final clash at The Emirates.
And Arsenal shareholder Morgan was clearly not impressed with what he was seeing from the Gunners on Sunday, despite hailing Aubameyang’s display.
Morgan wrote on Twitter: “At least we have Aubameyang.
“One tiny slither of hope & excitement amid a sea of putrid mediocrity.”
The result left Arsenal in sixth place in the Premier League table and looking as if they will miss out on a top four finish for the second season running.
MORE: Man United latest news
MORE: Arsenal latest news
MORE: Chelsea latest news
MORE: Liverpool latest news