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.
8 - No player has scored more Premier League North London derby goals than Harry Kane (8, level with Emmanuel Adebayor). Ruthless. pic.twitter.com/AYR6KmJ3J0— OptaJoe (@OptaJoe) December 2, 2018
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.
What does it mean? Gunners clamber into top four
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.
10 - Pierre-Emerick Aubameyang is the first player to score with 10 consecutive shots on target in the Premier League since October 2007 (Benni McCarthy for Blackburn). Pinpoint. pic.twitter.com/CHa1Tjyzfb— OptaJoe (@OptaJoe) December 2, 2018
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.
Key Opta facts
- Arsenal have found the net at least once in each of their last 23 home games against Spurs in all competitions, since a goalless draw in November 1998.
- Tottenham have dropped more points from winning positions in Premier League games against Arsenal than any club has against another in the competition (40).
- The Gunners have scored more second half goals than any other team in the Premier League this season (24).
- Torreira scored his first ever Premier League goal for Arsenal – the fourth player to do so in a match against Tottenham after Nicklas Bendtner, Mikael Silvestre and Per Mertesacker. Meanwhile, Emery's substitutes have scored (eight) and assisted (seven) more Premier League goals than replacements from any other side this season.
- Vertonghen's red card was Spurs' sixth in the Premier League against Arsenal – more than they've had against any other side in the competition.
Arsenal head to Old Trafford to take on Manchester United on Wednesday, while Spurs are back at Wembley, where they face struggling Southampton.