The Gunners got one over on their London rivals at Wembley, having fallen a goal behind when Blues star Christian Pulisic converted from close range in the fifth minute.
Almost 25 minutes later, Aubameyang was brought down in the box by Chelsea captain Cesar Azpilicueta and referee Anthony Taylor pointed to the spot, allowing him to equalise from 12 yards.
And with just over 20 minutes remaining, the Gabon international turned home the winner to hand Mikel Arteta his first trophy as a manager.
Following her husband’s breathtaking display at Wembley, Alysha Aubameyang took to Instagram to congratulate him.
Along with pictures of Aubameyang and Arsenal stars celebrating their win, Alysha wrote: “Congratulations my bbey # so proud of you”.
She then posted a picture of the striker standing next to the trophy on her story and said: “Too proud of you my bbey”.
Aubameyang proved crucial in Arsenal’s 14th FA Cup win, also scoring twice in their semi-final victory over Manchester City.
However, it remains to be seen whether the 31-year-old commits his future to Arteta’s side after entering the final year of his contract.
It is believed Barcelona, Real Madrid and Inter Milan are circling amid doubts over his future in north London.
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When asked if he could provide an update on his contractual situation after the win, Aubameyang said: ““Nothing. Just today and the trophy. That's it!”
But Arteta is determined to keep hold of his star man, insisting he has plans to build his Arsenal squad around him.
”He knows what I think about him. I want to build the squad around him. I think he wants to stay and it is just about getting the deal done,” the Gunners boss said.
“But I think these moments will help him to realise and believe that we are in the right path and he is a big part of that.
“He is loved by everybody at the club. Hopefully he can continue with us."
When asked if Aubameyang will extend his stay at the Emirates, Arteta said: ”I think he will, yes.”