Matt Taylor scored his first ever Bolton goals in a dramatic first half that saw Abou Diaby red carded for an horrific tackle on Gretar Steinsson.
But despite laying siege to the visitors goal in the first 15 minutes of the second half, Wanderers couldn't get a third goal.
And a double substitution by Arsene Wenger helped turn the game, bringing on Emmanuel Adebayor and Theo Walcott.
The duo gave Arsenal a badly-needed attacking edge and within six minutes the Londoners were back in the game.
Unmarked William Gallas fired home after Ivan Campo failed to cut out Cesc Fabregas' in-swinging corner.
Four minutes later, Steinsson felled Alex Hleb and Robin van Persie converted from the spot.
Bolton never looked likely to make their own comeback and it was no surprise when they conceded a third goal.
Fabregas' shot initially hit Andy O'Brien which then in turn deflected off Jlloyd Samuel.
Cue scenes of jubilation on and off the pitch with anyone connected with Arsenal as the Gunners live to fight another day in their battle with Manchester United and Chelsea.
Wenger reacted to Arsenal's recent poor league form by dropping top scorer Adebayor to the bench.
The Togo international hadn't scored in his previous six Premier League outings and, to add insult to injury, his arch rival, Nicklas Bendtner, replaced Adebayor.
There could have been a serious injury to Icelander Steinsson due to Diaby's challenge.
It was every bit as bad as Birmingham City's Martin Taylor's tackle on Eduardo da Silva last month, but Wenger somehow managed to remonstrate with the fourth official.
Steinsson, whose leg was lucky not to be broken, was bizarrely jeered by Arsenal supporters when he touched the ball.
Arsenal had the territorial advantage early on but couldn't create worthwhile opportunities.
Van Persie went closest with an angled left-foot shot, while Bendtner's poor control prevented him testing Ali Al-Habsi.
Meanwhile, in their first meaningful attack Bolton hit the front as Steinsson produced a superb cross from the right and Taylor stole in ahead of Kolo Toure to head that elusive first goal.
Taylor previously hit the net from the penalty spot against Bolton back in August.
However, his last goal from open play came 11 months ago in a 2-1 win over Newcastle.
And just like buses, the goals came in twos - albeit with a deflection off William Gallas.
Mathieu Flamini was dispossessed by a combination of Gavin McCann and El Hadji Diouf and they set-up Taylor, whose left foot drive clipped Gallas and deviated away from Manuel Almunia.
A combustible first half erupted again just before the break when Arsenal complained McCann's challenge on Philippe Senderos deserved a booking.
And when Kevin Davies slid in on the Swiss international to receive a caution from Chris Foy, Toure was booked for dissent.
There was no let up in the drama after the interval and Manuel Almunia's save from Gary Cahill on the hour proved pivotal.