Arsenal suffered their first-ever defeat at the Reebok Stadium as Bolton got their tactics spot on to severely damage their opponents' title hopes.
Bolton's deserved win leaves Arsenal 10 points behind leaders Chelsea.
Stelios Giannakopoulos stole in at the far post to head Bolton's winner after keeper Manuel Almunia failed to collect El-Hadji Diouf's teasing cross.
Robin van Persie came closest for Arsenal, but saw two efforts well-saved by Jussi Jaaskelainen.
However, it was Arsenal's keeper who was the busier as Bolton carried out Sam Allardyce's obvious instructions to attack the visitors aerially.
And a lively Diouf duly provided the questions which Almunia failed to answer.
The Senegal international wasted little time in testing whether the Spaniard is less error prone than Jens Lehmann, the man he has replaced.
Diouf provided an almost constant supply of crosses, as he targeted another chink in the Arsenal defence, the nervous-looking Justin Hoyte at right back.
Time and again Almunia flapped and hesitated - crashing into team-mates Sol Campbell and Patrick Vieira in one instance.
After another missed cross Gary Speed sent a shot over the bar, with the Spaniard stranded.
Credit must be given to Hadji for the teasing cross which led to Bolton's goal, but Campbell will be unhappy with his defending.
First the England defender weakly hooked a half-clearance and then allowed Diuof to get past and deliver his centre.
And Almunia once again proved unreliable as Giannakopoulos was left in space to nod home with ease into an empty net.
Diouf had already delivered a cross into the box which narrowly evaded Kevin Nolan by then.
And later, Nolan almost converted when the entire Arsenal defence, aside from Cole, allowed him to run free on to a loose ball.
Earlier in the day Chelsea moved 10 points clear at the top of the table and set a Premiership record by winning their sixth consecutive match without conceding.
In contrast, Arsenal's defence of their title appears destined to fail because of their porous defence.
But Bolton looked solid at the back - keeping Arsenal at bay in the first half aside from one clear-cut chance in the first half when Van Persie turned and shot straight at Jaaskelainen.
But Arsenal's response after the interval almost resulted in an immediate equaliser.
However, Jaaskalainen kept out Van Persie's close-range shot and Robert Pires headed the rebound wide.
Bolton, though, gradually took control of the game.
And Gianakopolous broke free after latching on to Ricardo Gardner's throughball but steered his effort over the bar.
Arsenal continued to look shaky, and Bolton's fans roared their team's every corner.
Midway through the second half Arsenal brought on Dennis Bergkamp and Jose Antonio Reyes.
Van Persie, who had been well-marshalled by Bruno N'Gotty, and Cesc Fabregas, who had lost his midfield battle with Jay-Jay Okocha, made way.
As the Gunners searched for an elusive equaliser, Bolton launched a counter-attack.
Diouf turned Campbell inside out but pulled his shot wide when it appeared he was about to make certain of the points for Bolton.
Arsenal offered little offensively, with Henry's shot easily smothered when he perhaps should have pulled the ball back to Freddie Ljungberg.
The French striker tried his luck again with a free-kick late on, but Bolton were not to be denied.
Bolton: Jaaskelainen, Hunt, Ben Haim, N'Gotty, Gardner, Campo,Okocha (Pedersen 79), Speed, Nolan (Hierro 87), Diouf,Giannakopoulos.
Subs Not Used: Poole, Vaz Te, Fadiga.
Booked: Nolan, Giannakopoulos.
Goals: Giannakopoulos 41.
Arsenal: Almunia, Hoyte, Toure, Campbell, Cole, Ljungberg,Vieira, Fabregas (Reyes 66), Pires, Van Persie (Bergkamp 66),Henry.
Subs Not Used: Lehmann, Senderos, Clichy.
Booked: Van Persie.
Ref: M Clattenburg (Co Durham).