Chelsea came on after five minutes after Christian Pulisic, but Arsenal came back in the middle of the first half when Aubameyang was sacked by Cesar Azpilicueta in the Chelsea box.
The striker converted from the penalty spot and although Chelsea started the second period strongly, it was captain Aubameyang who gave Arsenal the lead when he found some space in the box and produced a chip with force on Willy Caballero.
Chelsea went from bad to worse for Chelsea as Mateo Kovacic received a second yellow card after the third goal of the match.
The victory gave the Gunners the fourteenth FA Cup trophy and fourth since 2014.
He also gives Mikel Arteta, who has twice won the FA Cup as a player with Arsenal, his first piece of silver as the club’s manager.
Aubameyang praised his head after the final whistle.
“He deserved that victory,” Aubameyang told BBC Sport. “He did a fantastic job, and we’re all happy to have him on board and we’re just following him.”
In the first final ever played without fans, Chelsea started the brighter of both sides when Mason Mount received the ball in the Arsenal box and found Olivier Giroud.
The Frenchman beat Pulisic, who lifted his shot over Emi Martinez to become the first American to score in the FA Cup final.
The Blues continued to attack until the break of the first half of the drinks, after which they advanced to Arsenal and Aubameyang helped level the game when he advanced to the Chelsea goal and fell under the challenge of Azpilicueta, burying the resulting result in the lower right. from Caballero’s goal.
Hector Bellerin came in from the middle of Chelsea and, despite losing possession, the ball fell to Nicolas Pepe. He found Aubameyang, who broke into space and hit the ball on Knight.
Chelsea continued to push for a draw despite losing to Kovacic, but Arsenal held on to victory.
The result means the Gunners qualify for the Europa League despite finishing eighth in the Premier League.