The Arsenal star, 29, struck twice as the Gunners came from behind to win 4-2 in the explosive clash against Mauricio Pochettino's side.
However images from the game show that the striker had a banana skin thrown at him after scoring.
A Metropolitan Police statement today confirmed the arrests.
It read: "Four men have been charged following the Arsenal vs Tottenham football match at the Emirates Stadium on Sunday, 2 December.
"Paul Wright, 41 of Talbot Place, Bexley was charged with a public order offence and has been bailed to attend Highbury Corner Court on Monday, 31 December.
"Averof Panteli, 57 of Borrowdale Drive, Norwich; Charlie Watts, 26 of Goldring Court, St Albans and Jason Gannon, 36 of Gargery Close, Gravesend, Kent were charged with throwing a missile onto a football pitch.
"These charges relate to three separate incidents during the match. All three were bailed to attend the same court on Tuesday, 18 December. Enquiries continue.
"A total of six arrests were made in relation the match – four were dealt with as above; two other men were released with no further action."
As Aubameyang celebrated netting his first goal from the spot in front of the Spurs fans, the banana skin was launched in his direction.
It is not known if the incident was connected to racism.
But a Spurs spokesman said: “Behaviour such as this is completely unacceptable and the supporter in question will be issued with a ban.”
Two Gunners fans were also arrested for letting off smoke canisters during the match.
And both clubs face an FA probe after their players and staff were involved mass BUST-UP on the touchline following Eric Dier’s equaliser on the half-hour mark.
Harry Kane gave the visitors the lead in the first half before the Gabon striker's second.
That was followed by two goals in three second-half minutes from Alexandre Lacazette and Lucas Torreira earned Arsenal the points.
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