Mikel Arteta’s side made it 11 wins from 13 league games thanks to a close-range finish from Brazilian defender Gabriel in the second half at Stamford Bridge.
The Gunners are two points clear of second-placed Manchester City after the champions briefly took pole position with a win against Fulham on Saturday.
With only one round of games remaining before the World Cup brings the Premier League to a halt, Arsenal have emerged as genuine contenders to end City’s grip on the tite.
After beating Tottenham and Liverpool at home earlier this season, winning in west London was another significant statement from Arsenal as their unexpected challenge gathers pace.
This was an even sweeter victory than their other landmark successes this term as it came at the expense of former Arsenal star Aubameyang.
Aubameyang was anonymous in his first meeting with his old team since he was stripped of the captaincy and sold to Barcelona in January after Arteta lost patience with the Gabon forward’s repeated disciplinary issues.
Exiling Aubameyang has proved an inspired move by Arteta as Arsenal look a far more unified and determined group without the sulking striker.
Booed by the travelling Arsenal fans, Aubameyang was so underwhelming that it might not be long before he becomes unwelcome at Chelsea as well.
Chelsea boss Graham Potter might also be feeling the heat soon after his side’s winless league run extended to four games with a second successive top-flight defeat, prompting jeers from Blues fans at full-time.
Seventh-placed Chelsea lacked Arsenal’s urgency and now trail the leaders by 13 points, with even a top four finish far from certain.
Arsenal have not won the title since Arsene Wenger’s Invincibles in 2004, but no Gunners team has amassed more points at this stage in the Premier League era.
Facing the latest test of their title credentials, Arteta’s men were quickly into their stride, probing the Chelsea defence with authority and intent.
Ben White fired narrowly wide from the edge of the area after a flowing move cut through the Blues rearguard.
Snapping tigerishly at Chelsea, Arsenal were first to every 50-50 ball.
Gabriel Jesus robbed Ruben Loftus-Cheek and the Brazilian’s menacing run took him into the Chelsea area before Thiago Silva snuffed out the danger with a superbly-timed sliding tackle.
Aubameyang struggled to make any impact and lost his cool with a reckless lunging foul on White that earned a booking from Michael Oliver.
Gabriel Martinelli was a constant threat and his floated cross picked out the unmarked Jesus, whose face was a picture of frustration after his diving header missed the target from just six yards.
Aubameyang’s booking had raised the temperature in an increasingly fractious encounter.
Bukayo Saka was accused of diving by Potter after failing to win a foul when he went to ground after a shoulder barge from Marc Cucurella.
Arteta joined a furious exchange between the two coaching staffs and Saka responded by scything down Cucurella moments later as the Arsenal star was booked.
Having managed just four touches in the first half, Aubameyang finally had a sight of goal after William Saliba’s miskick but the Arsenal defender recovered to block the shot.
Played in by Saka’s deft pass, Jesus forced a good save from Edouard Mendy and from the resulting corner Arsenal took the lead in the 63rd minute.
Chelsea’s defending was woeful as Saka’s delivery was missed by three Chelsea players before Gabriel reacted fastest to poke home on the goal-line.
The sight of Aubameyang being substituted moments after Gabriel’s goal only added to the glee among the Arsenal fans crammed into one corner of the Shed End as they start to dream of title glory.