The incident happened when the Gabon striker celebrated in front of the travelling Tottenham fans as Arsenal ran out 4-2 winners against their North London rivals.
A supporter was arrested after a steward immediately identified the alleged culprit in the stands.
It is not known if the incident was connected to racism.
A Spurs spokesman said: “Behaviour such as this is completely unacceptable and the supporter in question will be issued with a ban.”
And now Aubameyang has spoken out on Instagram with a brief message.
Alongside a picture of the striker with the banana visible on the pitch, he wrote: "#Whysmandoingthis?"
The supporter was being questioned by police on Monday while Spurs have vowed to ban him at least until the outcome of the police investigation.
Ex-Arsenal striker Ian Wright condemned the fan when he was talking on BBC's Match of the Day.
He said: “It’s ironic really in a week where I present a show celebrating the pioneers and how far we’ve come,
“I’ve played against Spurs and I’ve taken a lot of abuse from Spurs, but never, ever has it been racial. Now Spurs have to deal with this because some idiot has done that.
“It’s not only embarrassed Spurs but it has embarrassed the Premier League because it has gone around the world, and now Spurs have to deal with that and have that tainting all over them. It’s really unfortunate to see.”
The FA will not investigate the incident as it has been handed over to the police.
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