A 41st minute goal by Greek international Stelios Giannakopoulos was enough to deny an Arsenal side that at times flattered to deceive.
Much of the midfield play was neat and creative, but the Gunners' frontrunners failed to cash in on the opportunities.
Jussi Jaaskelainen in the Bolton goal was also in impressive form, but it was El Hadji Diouf who stole the show.
He set the goal up for Giannakopoulos, went close himself on a number of occasions and in general created mayhem in an Arsenal defence that at times looked ragged and totally disorganised.
If Chelsea's strong defence seems to be taking them to the title, then the Gunners backline is certainly throwing it away if they are to be judged on this performance.
Both sides paraded more familiar line ups following their FA Cup activities last week.
But while Arsenal were given a tonic with the return from injury of Sol Campbell, Ashley Cole and Fredrik Ljungberg, Wanderers suffered a double injury blow that robbed them of two of the most potent players.
Central defender Radhi Jaidi, who has been devastating at set-pieces this season - he scored against Arsenal in a 2-2 draw earlier in the season - and frontman Kevin Davies, were both ruled out with hamstring strains.
Israeli international Tal Ben Haim partnered Bruno N'Gotty at the heart of the defence, while Diouf moved inside to lead the attack.
Arsenal, winners of their last three away games in an unbeaten run of seven Premiership matches, restored Ljungberg alongside Thierry Henry in their attack while Spanish keeper Manuel Almunia was again preferred to Jens Lehmann.
The Spaniard, however, was almost caught out in the fifth minute when good work by Diouf ended with the ball being flashed across the six-yard box, where Almunia just managed to scramble it away for a corner with Giannakopoulos threatening.
Arsenal's midfield responded with neat passing movements that created openings, but Henry and Robert Pires could not take advantage, although when Patrick Vieira decided to take matters into his own hands, his 25-yard shot was only inches too high.
Robin Van Persie was booked for a 23rd minute foul on Diouf and then Arsenal were lucky to escape when Gary Speed fired in a high velocity shot that skimmed the crossbar.
Van Persie, though, had a good chance to give Arsenal the lead in the 39th minute, but could only fire straight at Jaaskelainen.
That proved expensive as two minutes later, Wanderers were in front.
That was due to the persistence of Diouf who tricked and teased the Arsenal defence before crossing to the far post from where Giannakopoulos headed past a stranded Almunia.
And it should have been 2-0 on the stroke of half-time when a mix-up between Campbell and his keeper let in Kevin Nolan, but he was not able to keep his shot down and the ball failed past the angle of the upright and bar.
Jaaskelainen had to be alert to deny Arsenal at the start of the second half, racing out to smother the ball at Ljungberg's feet.
And the keeper, who has been linked with a possible move to Highbury, did well a few minutes later blocking Van Persie's shot, before Pires headed the rebound wide.
Wanderers responded with a near miss of their own, Jay-Jay Okocha and Diouf doing well only for Nolan to head wide, before Giannakopoulos was only inches away from adding a second after Okocha had split the Gunners defence again.
Both sides produced some stirring end-to-end entertainment.
Diouf, the game's most dangerous attacker, outwitted the Arsenal defence in the 70th minute, but he thundered his shot narrowly wide.
Ivan Campo could have savoured glory had he not shot straight at the keeper while at the other end a series of Arsenal corners called for some hard work by the home defence.
Vieira managed to beat the impressive Jaaskelainen only to see his shot go the wrong side of the post, as Bolton held on for all three points.
Man of the Match: El Hadji Diouf - Created the winner for Giannakopoulos and tormented the champions throughout to ensure that Bolton pulled off a minor shock.