The supporter launched the banana skin at the 29-year-old at the Emirates yesterday after the striker broke the deadlock in the tenth minute from the penalty spot.
He was subsequently arrested by the police after a steward immediately identified the culprit in the away section.
There were in total seven arrests made by the Metropolitan Police, with four men being charged, as Tottenham lost 4-2 against Unai Emery's men.
A Spurs spokesman said: “Behaviour such as this is completely unacceptable and the supporter in question will be issued with a ban.”
Aubameyang took to Instagram following the victory where he posed a picture of himself next to the banana, where he said: "#whysmandoingthis?"
Ian Wright slammed the Tottenham fan when speaking on Match of the Day 2, as he vented his anger.
Aubameyang netted twice against Spurs yesterday to take his goal tally to 12 strikes in all competitions.
While Alexandre Lacazette and Lucas Torreira also got in on the act as Arsenal leapfrogged Mauricio Pochettino's side into fourth spot.
And they will be looking to carry on their good form when they face Manchester United at Old Trafford on Wednesday night.
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