Christian Pulisic gave the Blues a deserved lead early on, but Aubameyang's penalty and a wonderfully worked second goal were enough to snatch the silverware.
While it was a remarkable performance from Mikel Arteta's men, the officiating did not help the course of the game. Chelsea lost Mateo Kovacic to a red card, while they also witnessed Pedro, Cesar Azpilicueta and Christian Pulisic hauled off due to serious-looking injuries.
On that note, we delve into the major talking points from Arsenal's historic 14th FA Cup triumph.
#1 Dicey Arsenal hand Chelsea the early lead
The entirety of the first half, barring the last few minutes was a wide open-ended game with both sides equalling each other's energy.
Arsenal's front four carried on a relentless press throughout, but the West Londoners were the ones to draw first blood.
Within about three or four minutes, they settled into the game and played in between the two Arsenal central midfielders. As one would have noticed for the opening goal, Jorginho was offered too much time to turn, take a couple of touches and then squeeze a pass to Pulisic.
The youngster, as tricky as he always is, proved to be a menacing presence for the opposition with his change of pace and acceleration. He played Mount in, whose left-footed pass fell to the the path of Giroud.
The Frenchman once again displayed just how selfless and intelligent he is inside eight-ten yards of the goal. A wonderful flick served Pulisic, who then took his chance with aplomb to punish a static Arsenal midfield.
#2 Arsenal up the tempo as Aubameyang scores
Arsenal grew into the game as minutes wore on, mainly making it happen through 50-50 wins, strong aerial challenges and retention of the ball.
The Gunners were at it immediately, with the front three and Ceballos clouding in on the Chelsea back three and forcing them to play long. They'd follow it up with a high, congested back line that disallowed the likes of Giroud to win the headers.
It was a clear-cut plan from Arteta's side, who often also chose to go long through Chelsea's right side. That, in fact, was their route to the leveller, as Aubameyang was played in smartly. What was wiser was Aubameyang's pace and full use of Cesar Azpilicueta's lack of it.
He cleverly won the penalty and dispatched it imperiously. Through the course of those few minutes, Arsenal gave Chelsea a very hard time defending with a bombardment of crosses towards the far post.