Kepa Arrizabalaga could only palm a Jorginho backpass off his own line, and Pierre-EMerick Aubameyang teed up Smith Rowe for the only goal of a tight London derby at Stamford Bridge.
While Chelsea remain favourites to secure Champions League qualification, should West Ham and Liverpool win their games in hand, the Blues will be under pressure to win their remaining two League matches while also preparing for their FA Cup and Champions League Finals.
The result leaves Thomas Tuchel’s Blues effectively facing four finals to end their season on a high.
As for Arsenal, Mikel Arteta will hope this is a win to build on as the Gunners face a summer rebuild following a disappointing campaign.
Kepa started in goal as Chelsea made seven changes as Tuchel rotated to handle a hectic schedule.
Arteta made five changes from Arsenal’s 3-1 win over West Brom on Sunday, with Pablo Mari, Thomas Partey, Kieran Tierney, Martin Odegaard and Pierre-Emerick Aubameyang all in from the off.
Both sides started competently, but the first half was a tale of two defensive errors.
Kai Havertz stole in as Pablo Mari dallied on a loose ball, with the German racing clean through on goal – but the German, who missed two sitters against Real Madrid here last week, blazed over the bar with the goal at his mercy.
Following that let-off, Arsenal capitalised on a howler from Chelsea 15 minutes in.
Smith Rowe put Arsenal in front after 15 minutes, capitalising on a loose ball from Jorginho in a rare defensive lapse from Chelsea.
Under pressure from a high Arsenal press, Jorginho played a blind backpass towards his own goal that left Kepa scrambling, and the goalkeeper was only able to parry the ball to stop an own goal.
Pierre-Emerick Aubameyang recovered possession and teed up Smith Rowe for a scuffed finish to put the Gunners into the lead.
Chelsea pushed and pushed in search of an equaliser but were unable to get back on level terms before half-time.
Arsenal took a 1-0 lead into the break but had to ride their luck to do that, with Mason Mount unlucky not to find the net on a number of occasions.
Christian Pulisic thought he had levelled 20 minutes into the second half, but was correctly flagged offside after turning home a corner flick-on from close range.
The Blues also came close as Bernd Leno tipped a Kurt Zouma header onto the bar before Olivier Giroud hit the woodwork on the follow-up in the 90th minute.
Unfortunately for Chelsea, that was the closest they get to an equaliser as Arsenal left west London with all three points to ensure the Blues face a nervy run-in.