Second-half goals from Sylvain Wiltord and Robert Pires looked to have put victory out of the home side’s reach but they battled back to set up a frantic finale that had Arsenal more than a little concerned.
Youri Djorkaeff pulled one back in the 74th minute before substitute Martin Keown cost his side valuable points in the title race with Manchester United by heading into his own net six minutes from time.
And the action was not over then as Wanderers had central defender Florent Laville sent off a minute from time for a second bookable offence.
Bolton, with five clean sheets from their last six games, were happy to name the side that held Blackburn to a goalless draw five days earlier.
That meant Ricardo Gardner keeping his place in a Wanderers defence that certainly for the first half, kept a tight grip on the Arsenal front runners.
In fact during the first period Wanderers kept the champions in check and even managed to cause a moment or two of anxiety in the Gunners rearguard.
Jay-Jay Okocha was the first to test David Seaman, back in the Arsenal goal after injury, only to see his shot turned away.
Yet the first real opening came at the other end when Ivan Campo was robbed in midfield by Ray Parlour and when the ball was played into the six-yard box, Fredrik Ljungberg was only inches away from getting a touch.
That sparked some attacking action from the home side and Henrik Pedersen, having taken advantage of a deflection off the referee, saw his shot flash across Seaman but just wide of the far post.
Okocha then came along to worry Seaman, who was relieved to see the Nigerian international's 20-yard free-kick deflected inches past a post.
All that did not seem to worry the champions unduly and they worked the ball well down both flanks to try and create openings.
Ljungberg should have done better when he found space to shoot in the area but fired tamely into the hands of Jussi Jaaskelainen and the same was true of Thierry Henry, who also lacked power in his shot to beat the Finnish international.
Within two minutes of the second half however, Jaaskelainen was beaten by a move generated by the pace of Henry.
The Frenchman exchanged passes with Pires then beat Bruno N'Gotty for speed to fire the ball across the keeper to the unmarked Wiltord, who tapped in from close range.
Bolton responded with their best move of the match when Per Frandsen forced Seaman into a finger-tip save but after 56 minutes the Gunners doubled their lead.
Again Henry and Pires masterminded the move after Frandsen had lost possession.
In the end it was Pires who was rewarded with the final touch leaving Jaaskelainen no chance.
Wanderers tried again to reduce the arrears but Seaman did not look in the mood to be beaten as he plucked out N'Gotty's header.
Yet Frandsen turned that around in the 74th minute when Wanderers managed to pull a goal back.
The Dane fired in a powerful shot that the keeper could only push into the path of Djorkaeff, who was able to prod the ball home.
Two minutes later, however, Seaman saved what looked to be the equaliser when he blocked Pedersen's close-range shot at the far post.
Pedersen then had another chance to put Wanderers clear following Gudni Bergsson's header into the six-yard box, but again saw his effort blocked.
Six minutes from time, Wanderers were rewarded but not in the way they expected as substitute Keown, under pressure from Bergsson, headed into his own net.
Yet the excitement was not over as Wanderers defender Laville was sent off in the 89th minute for a foul on Ashley Cole, his second yellow card.