John Terry and Eidur Gudjohnsen punished the champions' notorious vulnerability at dead ball kicks after Thierry Henry twice gave Arsenal the lead.
Chelsea have still not won a league game at Highbury since 1990. But they remain five points clear of third-placed Arsenal and four ahead of second-placed Everton.
They could have won the game through Frank Lampard and Arjen Robben in the second half - but they almost lost it in the dying minutes when Cesc Fabregas instigated two penetrating moves for the Gunners.
Arsenal have kept just one clean sheet in their last 17 games and their capacity for leaking goals on crosses is costing them dear.
Arsene Wenger continued with Manuel Almunia in goal, despite criticism of his shaky midweek performance against Rosenborg. Skipper Patrick Vieira was suspended, so youngsters Fabregas and Mathieu Flamini filled the central midfield roles.
Chelsea boss Jose Mourinho stuck with two wingers and Eidur Gudjohnsen as a lone striker.
Henry made an explosive start. He struck after 75 seconds, seizing on Jose Antonio Reyes' header and crashing a left-foot shot past Petr Cech.
Chelsea kept calm, kept pressing and levelled 16 minutes later. Almunia beat out Frank Lampard's shot for a corner. Terry ran in unmarked to bullet a header across Almunia. It was a replica of so many goals that Arsenal have conceded this season.
Arsenal have rarely backtracked so much in a home game as they did in the first half. At times, Reyes seemed like an auxiliary defender as they tried to reinforce central midfield. Pires also tucked in on the right and they were content to unleash Henry on the break.
Chelsea lived up to Mourinho's promise to try and win the game, but they were stunned in the 29th minute after Pires went down on the edge of the box.
Gudjohnsen was still lining up the Chelsea wall as Henry took a quick free-kick which deflected off Tiago and left Cech stranded.
Mourinho sent on Drogba and Wayne Bridge for the second half, going to four up front – and was rewarded when the Blues levelled within 30 seconds.
Gallas flicked on Lampard's free-kick and Gudjohnsen nodded past Almunia. Arsenal's defence was floundering again.
They left Lampard unmarked at another corner, but the midfielder wasted a free header, before Drogba missed another chance from a flag-kick.
Robben then drifted through the home defence, but shot into the side netting.
Arsenal fought back after Mourinho replaced Gudjohnsen with midfielder Scott Parker. Fabregas, a peripheral figure early on, was at the heart of the Gunners' response.
Henry missed a great chance to complete his hat-trick, firing over from Pires' cross after Fabregas split the defence.
Substitute Robin van Persie almost snatched victory six minutes from time, side-footing inches wide from another slide-rule pass by Fabregas.
Wenger must be delighted with his teenage midfielder, but will be worried sick about his side's defending.
Chelsea made them pay for it today.