Aubameyang scored twice with Alexandre Lacazette and Lucas Torreira also hitting the target as Arsenal won an explosive north London derby, with Tottenham scoring through Eric Dier and Harry Kane
But the game was marred by a mass brawl between the two teams, claims that two smoke canisters were thrown into the away end and the unpleasant incident involving Aubameyang.
The Gabon striker had just fired the Gunners in front from the penalty spot when a banana was thrown at him.
The Football Association confirmed they will be launching an investigation into the incident.
Missiles were also thrown during a melee which broke out when Dier celebrated his 30th-minute equaliser by running to the home fans and putting his finger to his lips.
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But a Met Police spokesman confirmed that of seven arrests made at the game for public order offences, only one was for an object thrown on to the pitch.
It is understood two of the arrests involved the lighting of smoke canisters. All those arrested were taken to a north London police station.
The FA will await referee Mike Dean’s report into events but both teams face a charge of failing to control their players after the bench-clearing brawl.
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Arsenal extended their unbeaten run to 19 games with this hard-fought comeback win, which helped them leapfrog their bitter rivals in the table.
But both managers played down the ugly melee between the players, which started when Arsenal substitutes warming up on the touchline took exception to Dier’s celebration.
Dier, who was booked, said: “I had my back to it all so I’m not too sure what happened. But this is football. It’s a derby. Football is all about emotion and I don’t understand how I can get a yellow card in that situation.
“It baffles me because if you take the emotion out of football you’re going to destroy the game for everyone.
“The ref said he gave me the yellow card because it was because of me that the whole thing started. If you watch it, we’re celebrating, I don’t leave the pitch at any point.
“And some of their players that are on the bench come to us. Their players approached us. I don’t know what’s wrong with it.”
Spurs manager Mauricio Pochettino, who raced out of his technical area to play peacemaker, said: “It’s football no? The emotion. In that moment it was to try to put the calm in my players.
“There was a massive fight there but I didn’t know what was going on. My intention was always to calm it. I don’t know if it was the celebration of Dier which upset people there.”
Arsenal boss Unai Emery said: “It was a moment of very big emotions. Heart. They were fighting a lot. We need also to be calm.”