The Blues got off to a slow start early on against the Gunners, allowing the visitors to take control and dictate possession.
It was a scrappy first half between the London clubs, both sides were not performing to their best but the biggest chance fell the way of Gabriel Jesus who failed to convert from Gabriel Martinelli’s cross.
17 fouls were awarded in the first half by referee Michael Oliver and the majority of it was against Chelsea.
After returning for the second half, a corner from Bukayo Saka beat the crowd and was destined to cross the line, until Gabriel Magalhaes poked home on the goalline.
Though Saka and Martin Odegaard had subsequent chances to get a second goal for Arsenal, the game ended 1-0 in favour of the Gunners.
The defeat was Chelsea’s second in a row in the Premier League and Graham Potter’s first as Blues boss at Stamford Bridge.
Arsenal are now two points over Manchester City on the Premier League table.