Pedersen had been dropped to the substitutes bench as Wanderers manager Sam Allardyce prefered the on loan El-Hadji Diouf who was making his full debut since his recent move from Liverpool.
Arsenal where looking for their sixth consecutive win of the season which would have stretched their unbeaten league run to 46 matches but the Danish international Pedersen struck with just minutes remaining.
The away side had contained their London opponents well in the first half, often frustrating the home side as they looked to build up their attacks through their danger trio of Thierry Henry, Jose Antonio Reyes and Robert Pires but more often that not they found the Bolton back line very hard to break down with the Tunisian international Radhi Jaidi appearing on top form.
On eight minutes Henry gave the Wanderers a warning sign of his offensive capabilities when he latched onto a clever hooked pass by Reyes but Jussi Jaaskelainen in the Bolton goal stood firmly to deny the current PFA Player of the Year the opening goal. The previously mentioned Jaidi also stood firm as Pires was to attempt the follow up shot.
Just before the quarter hour mark Kevin Nolan had a fantastic chance to add to his goalscoring account for the season with a swerving shot from a good 25-yards which sailed narrowly wide of Jens Lehmann's left post.
Henry made it second time lucky on the half hour when he slotted home the first goal of the game after the recently returned Patrick Vieira played a neat one-two with his fellow countryman. The ex-Monaco player made one of his famous runs through the channel in between Bolton defenders Nicky Hunt and Bruno N'Gotty before hitting the ball to Jaaskelainen's left.
Shortly before half time Henry was denied a second goal, Vieira crossed in from the left hand side to his fellow Frenchman but Jussi Jaaskelainen saved well after the forward was given a free header.
After half time Bolton made a double change with joint top scorer Henrik Pedersen and the experienced ex-Spurs striker Les Ferdinand coming on for Kevin Davies and the less effective El-Hadji Diouf and this seemed to spark the Lancashire side into life with the Trotters having a large majority of the possession share in the second period.
On the hour Arsenal forward Reyes was looking for his sixth consecutive goal which would have put him on a par with Arsenal greats Ian Wright and Cliff Bastin but the youngster could only see his shot go wide.
Just a few minutes later Bolton got a deserved equaliser when the impressive Jaidi rose above his marker to head home a bullet header past Lehmann following Okocha's pin point corner kick. However the jubilation was short lived as on 66 minutes the home side restored their lead thanks to an effort from Robert Pires who neatly finished following a good move down the right hand side which had seen Freddie Ljungberg get past Ricardo Gardner with a nice piece of skill.
Pires has often been a goalscoring thorn in Bolton's side in the past but it is fair to say that the French international knew very little about the low cross into the area which left the Bolton defence at sixes and sevens.
Arsenal despite gaining back their advantage made changes with Edu replacing his fellow Brazilian Gilberto Silva and Reyes departing the fray to be swapped for the evergreen Dennis Bergkamp. Bolton brought on the veteran stopper Fernando Hierro in place of his tiring ex-Real Madrid teammate Ivan Campo.
With ten minutes to go Sam Allardyce was furious with referee Phil Dowd and his assistants after the Staffordshire official booked Bolton's Jamaican wing back Gardner for a high footed challenge on Ljungberg. Gardner appeared to win the ball whilst Swede Ljungberg looked to knock the ball forward with his head which appeared to be low.
Ljungberg then had a half chance following some impressive play by Bergkamp but with just five minutes of play to go on the clock Wanderers snatched a deserved point to end the Gunners 100% start to the season.
Bruno N'Gotty floated in a free kick from the right hand side and this was flicked on by the hardworking Ferdinand finding it's way to Pedersen who tucked the ball into Lehmann's left corner much to the delight of the travelling Bolton support.
Wanderers had worked very hard to frustrate Arsenal and deserved something out of the game given a sturdy second half. Often the officiating went against the Trotters but this did not deter them from the job in hand. Having lost out to Manchester United late on last week it was nice for the Wanderers to be on the positive of some late drama.
Five points from a possible nine against Liverpool, Manchester United and Arsenal is no mean feat, especially given the latters impressive surge into the history books.