The German was absent for the Gunners' dramatic win over Tottenham in the first north London derby of the season on Sunday having previously missed his side's Europa League clash with Vorskla Poltava in Kiev.
A Tottenham spokesman said: "Behaviour such as this is completely unacceptable and the supporter in question will be issued with a ban".
A further six arrests were made due to public order offences, including two Arsenal supporters who lit smoke canisters inside the stadium during the match.
An early penalty kick goal from Pierre-Emerick Aubameyang gave the Gunners a lead, but Tottenham came back quickly.
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The win sees Arsenal move fourth, ahead of Spurs on goal difference, with Unai Emery now focused on another testing examination away at Manchester United in midweek.
"It was a very competitive game, it's tough for us because the fixture was after Chelsea and Inter Milan, it didn't help us, but the team was very competitive", Pochettino told Sky Sports.
"But above all it is three points, like against Bournemouth". We're not happy and yesterday was no different.
This result might have moved Arsenal into the top four at their neighbours' expense, but considering the teams' schedules - as well as the fact that, against form, they won this fixture previous year - it would be hasty to talk about balances of power in north London yet.
Television replays showed a banana skin present on the pitch as Arsenal celebrated their opening goal, scored by Gabon global Pierre-Emerick Aubameyang from the penalty spot. Football needs these kind of games and if you try to ruin these games, then you're ruining football.