The Gunners began the game knowing that a two-goal margin of victory would take them to the summit of the Premier League table.
Bolton however did not read the script and took an early lead through Gary Cahill after just seven minutes.
The Gunners had begun brightly with a flurry of early shots on target, but they gave possession away too easily and failed to clear their lines.
Cahill received the ball at his feet and the tall defender turned to fire home left footed from just ten yards out. Arsenal then endured a nervous few minutes. They looked unsure in defence and every pass seemed to be over-hit.
Cesc Fabregas had a golden opportunity to level the scores on 12 minutes when he was slipped in on his own on the left side of the area by Tomas Rosicky.
The offside claims were not answered, but the Spaniard belied his recent goalscoring form by firing straight at Jussi Jaaskelainen from just three yards out.
Eduardo latched on to a long ball a minute later and his fierce shot drew gasps around the stadium as his 20-yard effort fizzed its way toward goal and shaved the top of the Bolton bar. The Gunners were raising the stakes in attack, but continued to look unconvincing at the back.
Andrey Arshavin then sent a half-volley inches past the left post, having begun the move himself when winning possession at the other end of the pitch.
Matt Taylor forced a saved out of Manuel Almunia in the 22nd minute when his free-kick went around the Arsenal wall and was creeping into the bottom left corner but for the Spaniard's outstretched right arm.
Arsenal's evening went from bad to worse when a careless lunge in the area by Denilson saw Chung-Yong Lee fall to the ground and referee Alan Wiley pointed to the penalty spot.
Taylor stepped up and sent the ball into the bottom left-hand corner of the net over Almunia's outstretched arm.
Eduardo missed a golden chance to reduce the arrears when he latched on to a defence-splitting Fabregas pass.
Unfortunately, the Gunners striker's turn and shot was straight at the Bolton keeper when either side of the Finn would have been a certain goal.
Bolton's luck kept them ahead when, in the 40th minute, a Fabregas free-kick into the area was headed back to his own goal by Kevin Davies. With Jaaskelainen well beaten, the visitors were relieved to see the ball bounce back off the bar.
Rosicky did reduce the arrears in the 43rd minute with a shot from the right side of the area that was hit so sweetly that it was past the Bolton keeper before he could react.
Jaaskelainen kept Bolton ahead a minute later when he made a great save from Fabregas. It was now Bolton's turn to get jittery. Owen Coyle could not wait for the half-time whistle to calm his troops down.
Arsenal drew level in controversial circumstances six minutes after the restart when Wiley failed to give a foul on Mark Davies when William Gallas appeared to miss the ball and followed through clumsily on the Bolton midfielder's ankle.
The ball fell to Arshavin who fed Fabregas who scored with a low shot from an acute angle on the right side of the area. The Spaniard almost added another three minutes later, but his dipping 20-yard effort was tipped over by the Bolton goalkeeper.
The Gunners took the lead in the 65th minute when Abou Diaby headed the ball down for Thomas Vermaelen whose instant left-foot shot from nine yards out gave Jaaskelainen no chance.
The Gunners were now going full pace for the two-goal cushion that would give them top spot. Bolton, though, still looked dangerous on the break and set-pieces, that menace further boosted by the introduction of Ivan Klasnic.
Arsenal's crucial fourth goal came in the 85th minute with a move that was begun by Gael Clichy on the left flank.
The left-back back-heeled the ball to Eduardo who returned the pass for Clichy to deliver the ball infield.
A succession of swift passes saw the Gunners work the ball to Arshavin who beat his man with a nimble turn before firing a low drive past Jaaskelainen.
Arshavin should really have made it 5-2 as a pass to an unmarked Theo Walcott would have led to a certain goal. Instead, the Russian, who had broken from his own half, took too long to shoot and allowed Jaaskelainen to block his tame shot.
The final whistle eventually came after six long minutes of stoppage time and the Gunners were able to celebrate their status as the new league leaders.