The striker became the first Premier League player to reach 10 goals for the season before late strikes from Alexandre Lacazette and Lucas Torreira secured all three points for Unai Emery's rampant side.
Mauricio Pochettino's men, who saw Jan Vertonghen sent off late on, led 2-1 at half-time thanks to Eric Dier and Harry Kane, but the result sees them drop out of the top four at the expense of its north London rival.
The Gunners' dominant start was rewarded 10 minutes in, when Aubameyang swept home from the spot after Vertonghen intercepted a cross towards the six-yard box with a raised hand.
Spurs found themselves level with half an hour played, though, when Bernd Leno failed to keep out Dier's near-post header from a Christian Eriksen free-kick, after which a melee ensued among the Arsenal substitutes and Spurs' celebrating players.
Dier looked to be marginally offside and referee Mike Dean was in the spotlight again four minutes later, when he penalised Rob Holding for sliding in on Son despite minimal contact, allowing Kane to make it 2-1 from 12 yards.