A goal from Kevin Nolan was cancelled out by Kolo Toure in an all-action second half that was in complete contract to the opening 45 minutes.
Bolton have had more than their share of success against the Gunners in recent years and began the game showing that they knew it.
Sam Allardyce's men were on the attack from the opening whistle and forced a save out of Manuel Almunia within the first minute when the keeper held a Kevin Davies header.
The Gunners began to show glimpses of what they can do and Matthieu Flamini was just inches away from getting his foot to the ball in a goalmouth scramble that was quelled by a brave Jussi Jaaskelainen on ten minutes.
Theo Walcott tested the keeper with a shot from the right side of the area when the youngster had breezed past Ricardo Gardner.
Such was the ferocity of the shot that Jaaskelainen spilled the ball in front of him, but there were no Arsenal strikers in place to take advantage before the keeper pounced to gather at the second attempt.
With the sides cancelling each other out, the game only really warmed up in the last five minutes of the first half.
The Gunners and their fans were fired up by an audacious effort by Thierry Henry that was thwarted by some equally intelligent defending by Abdoulaye Meite.
Henry got to the ball before it bounced into the arms of Jaaskelainen and tried a cheeky back-heel that was cleared off the line by Meite.
While the momentum of the game looked to be swinging in Arsenal's favour, the visitors were the ones who took the lead five minutes after the restart.
The Gunners failed to deal with a long ball into the area which was only half cleared and found its way back to Nicolas Anelka on the right side of the area. The former Gunner then slipped a ball through into the path of Davies who drilled a low ball across the Arsenal goal which Nolan fired home.
Arsenal re-doubled their efforts after falling behind but did not look like scoring despite having the lion's share of possession.
Henry had a golden opportunity to level the scores on 65 minutes when the tireless Emmanuel Adebayor chased a ball down on the left flank before squaring, but the skipper's shot was charged down by the Bolton keeper.
Arsene Wenger then took a gamble on 70 minutes by taking off defender Justin Hoyte and replacing him with Carling Cup hero Julio Baptista.
The gamble paid off, but it was defender Toure who got the Gunners back into the game on 78 minutes after Meite had given away a free-kick on the right side by hauling down Cesc Fabregas.
The young Spaniard delivered a ball into the area which was headed backwards by Nicky Hunt towards the far post where Toure was well placed to send a diving header into the roof of the net.
Baptista should have done better just four minutes later when he rose highest to meet a Fabregas free-kick but he headed well wide of the target.
Jaaskelainen then claimed a well-struck shot form Aliadiere at the death which helped his side claim a draw and a replay at the Reebok.