Caretaker Trotters manager Archie Knox would have been proud of his charges who contained the Gunners for much of the match, but the cream rose to the top in the end.
Arsenal should have taken the lead after just nine minutes when Emmanuel Adebayor had just the goalkeeper to beat from inside the area following some good work by Emmanuel Eboue on the right flank. Unfortunately, the Togolese striker sliced his shot well wide.
The bulk of the first half was a scrappy affair. Arsenal, trying to play were doing so in patches while Bolton, trying to spoil, were more successful. Bolton's desire to play prettier football seemingly left along with Sammy Lee.
The deterioration of the game and the development of a fractious niggly feel to the match suited the visitors. Referee Mike Riley made some early bookings and his whistle seemed to be permanently lodged in between his lips.
Adebayor wasted another opportunity on 42 minutes when Eduardo skipped past a couple of Bolton defenders on the right flank before delivering a cross onto the head of his strike partner who was waiting at the far post.
The ball took an age to come down and the tall striker mis-timed his header as he guided the ball into the ground and wide of the right post.
The Gunners were simply not being allowed to play and the new strike partnership of Adebayor and Eduardo was starved of chances.
Eboue could have got the Gunners off to the best of starts two minutes into the second half but fired high and wide from the right side of the area.
Cesc Fabregas' 25-yard dig on 53 minutes was comfortably claimed by Jussi Jaaskelainen and Arsenal were missing Robin van Persie, ruled out by a knee injury which is likely to keep him sidelined for six weeks.
They lacked the ruthlessness in front of goal that had taken Arsene Wenger's players to the top of the table.
Bolton's industry and determination had a lot to do with Arsenal's containment, but the Gunners also had themselves to blame. A hurried pass here, a misplaced one there made for a poor spectacle and a lack of opportunities.
Those that did come were wasted, Adebayor being the main culprit, especially on 62 minutes when his shot from the edge of the area was fired well wide from the edge of the area when he should have at least tested the keeper.
The Arsenal manager introduced Theo Walcott and Tomas Rosicky in an effort to add some spark to the attack, Eduardo and Eboue being sacrificed. The gamble worked.
Arsenal came close to making a breakthrough on 65 minutes but Jaaskelainen showed his quality to deny fit-again William Gallas from close range.
The opening goal eventually came from a set-piece three minutes later. A free-kick was awarded to the Gunners 25 yards out.
Fabregas rolled it to Mathieu Flamini who teed the ball up for Kolo Toure and his low drive went through the legs of Ivory Coast team-mate Abdoulaye Meite and into the bottom left-hand corner of the net.
The goal seemed to settle the Arsenal team and crowd, both of whom were getting frustrated. Bolton too became more adventurous, which left more gaps to exploit.
Stelios Giannakopoulos, who has a good record against the Gunners, was also introduced to add bite to the Bolton attack, but it was the home side that scored next.
The Arsenal substitutes combined well on 80 minutes for the second goal. Walcott shook off the attentions of the Bolton defence to deliver a low ball into the box which the waiting Rosicky tapped in beyond the helpless Bolton keeper.
The Gunners celebrated another three points in a jubilant huddle that has become a tradition, but much of the jubilation was born out of relief.