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 their north London rivals.
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.
Lacazette and Aaron Ramsey came on at half-time and the latter helped the Gunners draw level, steering Hector Bellerin's pass to Aubameyang, who bent a sublime first-time finish past the static Lloris.
Chances came and went before Arsenal got the crucial fifth goal 17 minutes from time, when Ramsey robbed Juan Foyth and Lacazette's strike spun in off Dier's shin.
Torreira's first for the club followed three minutes later when he slotted past Lloris and celebrated with gusto.
Vertonghen was dismissed in the closing stages to compound a miserable day for the visitors.
Gunners clamber into top four
Emery's side are now ahead of Spurs on goal difference and the cushion to chasing sides Everton and Manchester United is eight points ahead of the Merseyside derby.
It is also only Arsenal's second win in nine league meetings with Spurs and comes after their fierce rivals so impressively dispatched Chelsea last weekend. If the balance of power had been shifting in north London recent seasons, this game showed there is little to split the teams.
Aubameyang setting new standards for clinical finishing
Aubayemang might not have been involved to a great extent in Arsenal's build-up play, but when you have a finisher as ruthless as he is, it matters little. The Gabon striker made it 10 goals from 10 shots on target in a row in the Premier League with his second in the derby. He then assisted Torreira's clincher.
Vertonghen loses his cool
Vertonghen's handball was a bizarre moment from the experienced defender, and a poor outing was compounded when a studs-up challenge on Lacazette in the 85th minute earned him a second yellow card.
