Mikel Arteta would have wanted his side to continue their winning run after recent victories over Liverpool in the Community Shield and Chelsea in the FA Cup - but the away side were to be triumphant.
Although Arsenal have not officially announced their starting XI, 13 different players were spotted across the 90 minutes in north London, most of which were first-team regulars.
Emiliano Martinez continued in goal for Arsenal having replaced Bernd Leno after his recent injury.
Full backs Hector Bellerin and Cedric also featured, with the former set to start in the right-back position at Craven Cottage next weekend.
They were joined in defence by Rob Holding, who has been linked with a move away from the club, and the recently returned William Saliba, who is set to battle for a regular starting spot.
In shock section for Arteta, Mesut Ozil featured in a midfield that included Dani Ceballos and Mohamed Elneny.
As well as Aubameyang and Alexandre Lacazette, Joe Willock, Willian and Nicolas Pepe made up the minimum list of 13 players that took to the pitch during the match.
The result will no doubt have been a disappointing one for the home side after their recent good form.
Spanish boss Arteta said after Arsenal beat Liverpool on penalties: “I’m so happy.
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“I knew the challenge we were facing today. Thank you to the players for the effort and the performance.
“The courage of the team [was the most pleasing], how aggressive we were without the ball and to break the pressure of Liverpool. I knew in the second half we would suffer.
“This generates belief, to be able to compete against a team like this in a final makes me happy.”