Chelsea took the lead after five minutes thanks to Christian Pulisic, but Arsenal came back strongly in the middle of the first half when Aubameyang was knocked down by Cesar Azpilicueta in the Chelsea box.
The forward converted from the penalty spot, and although Chelsea started the second half well, it was captain Aubameyang who gave Arsenal the lead when he found space in the box and produced a clever chip on Willy Caballero.
Things turned from bad to worse for Chelsea as Mateo Kovacic received a red card after a second yellow shortly after the game’s third goal.
Victory presented the Gunners with their fourteenth FA Cup trophy and their fourth since 2014.
It also gives Mikel Arteta, who has won the FA Cup twice as a player with Arsenal, his first piece of silver as a club manager.
Aubameyang praised his boss after the final whistle.
“He deserved this victory,” Aubameyang told BBC Sport. “He did a great job, and we are all happy to have him on board and we are following him.”
In the first ever final without supporters, Chelsea started the brighter of the two teams when Mason Mount received the ball in Arsenal’s box and found Olivier Giroud.
The French threw the ball at Pulisic, who lifted his shot at Emi Martinez to become the first American to score in the FA Cup final.
The Blues continued to attack until the drink break in the first half, after which the momentum shifted to Arsenal and Aubameyang helped level the game when he leapt to Chelsea’s goal and fell under the challenge of Azpilicueta, burying the resulting penalty in the lower right corner. of Caballero’s goal.
Full-back Hector Bellerin galloped through Chelsea’s half of the field and, although he lost possession, the ball fell to Nicolas Pepe. He found Aubameyang, who squirmed in space and kicked the ball at Caballero.
Chelsea continued to push for the equalizer despite Kovacic’s loss, but Arsenal held on for the win.
The result means the Gunners advance to the Europa League despite an eighth place finish in the Premier League.