It looked like Arsenal, who have won the Community Shield the last three times they contested it, were in for a disappointing day when Liverpool appeared to open the scoring through Virgil van Dijk after seven minutes.
However, the offside flag went up immediately and a replay showed that Van Dijk was well ahead of the Arsenal backline as Andy Robertson delivered in the cross.
Despite Liverpool enjoying 60% of the possession in the opening minutes, it was Arsenal who found the back of the net first through Aubameyang on 12 minutes.
The ball was carried up the pitch by Bukayo Saka who passed it to Aubameyang for a driving run down the left. Given time and space by the Liverpool defence, the Gabon international curled a perfect strike into the bottom right corner.
Aubameyang celebrated his goal with the iconic Black Panther salute in honour of the actor Chadwick Boseman who died from cancer on Friday.
Arsenal continued to advance with Alisson doing extremely well to push a shot from Eddie Nketiah around the edge of the post on 20 minutes.
Liverpool dominated towards the end of the half but failed to find the net with several shots skewing wide or over the bar of Emiliano Martinez's goal.
Roberto Firmino, who has eight goals in 10 matches against Arsenal, almost replicated Aubameyang's first-half goal on 51 minutes but saw his effort fall right and wide.
Brave goalkeeping from Martinez saw the ball smothered and another chance snuffed out for Liverpool.
Liverpool's tenacity paid off when the ball broke to substitute Minamino who scored his first goal for Liverpool on 73 minutes.
Arsenal protests for a handball off Mohamed Salah fell on deaf ears and several VAR replays showed no obvious signs of foul play.
Despite the London side visibly tiring as the game went on, neither side could find a goal and -- in the tradition of the Community Shield -- the match went straight to penalties.
"I'm so happy. I knew the challenge we were facing today," Arsenal head coach Mikel Arteta said after the game.
"The courage of the team [was the most pleasing thing], 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."