Arsenal's poor record at Bolton continued as a brace from Nicolas Anelka helped consign them to defeat.
Faye heads Bolton into the lead against Arsenal
Abdoulaye Faye headed Bolton ahead before team-mate Kevin Davies escaped a red card for pushing Emmanuel Eboue.
Anelka powered in a 25-yard screamer against his ex-club, who then pulled one back with a Gilberto Silva header.
Arsenal hit the woodwork three times in the course of the second half but their hopes were ended when Anelka raced clear and clinically angled in a shot.
Arsenal had promised to be more of a match for Bolton's physical approach ahead of the game following their recent struggles to combat the power of the Reebok Stadium side.
The visitors made a promising start as they seemed ready to back up their claims.
Theo Walcott's pace on the right-wing unsettled the Bolton backline and he crossed for Emmanuel Adebayor, who could only shoot straight at keeper Jussi Jaaskelainen after failing to make proper contact from six yards out.
Davies pushed Eboue but escaped with a yellow card
But Faye was allowed to make a run to the near post and head the home side into the lead from El-Hadji Diouf's corner as Bolton quickly asserted a stranglehold on the game.
In a familiar scenario between these two sides, Arsenal were being denied space and time while Bolton's main threat came from set-pieces.
The match developed into a fractious affair and Davies was fortunate to escape being sent off.
He followed up a rash challenge on Eboue with a push when the Arsenal right-back squared up to him to complain about the tackle.
The saving grace for Davies was that his hands were below shoulder height on Eboue and that is now deemed to warrant a yellow card rather than red.
Jaaskelainen twice beat Adebayor to the ball as Arsenal attempted to level but Bolton had rattled their opponents and carried the greater threat as they matched their hard-working game with a quality that is sometimes overlooked.
Diouf was Arsenal's chief tormentor and, after Quinton Fortune limped off injured for the hosts, Bolton extended their lead in an action-packed end to the first-half.
Anelka picked up the ball with his back to goal just outside the corner of the area before turning and powering in a stunning strike past stranded keeper Jens Lehmann.
Almost immediately, Silva headed in a corner at the other end to give Arsenal hope of a comeback.
The Gunners started the second half with a strong sense of determination as their stylish football began to have an effect.
Fabregas had a 20-yard shot scrambled away by Jaaskelainen before Walcott burst clear on the right and found Ljungberg with his cross.
The Swede stooped to head home only to see his effort crash off the crossbar to safety.
Bolton were still a danger on the counter-attack and Anelka had an effort scrambled to safety off the post by Lehmann before adding his second.
The French striker ran on to a slide rule Ivan Campo pass and finished with aplomb, despite a suspicion of offside about the goal, to all-but secure Bolton's fourth home win in five games against the Gunners.
Adebayor and Fabregas struck the woodwork as Arsenal continued to battle on but their efforts proved to be in vain.
Bolton boss Sam Allardyce:
"We knew this was a must-win match after throwing points away recently.
"Doing that against a team of Arsenal's quality was always going to be a big task but we have done it again.
"It was a really great victory at a difficult time and gives us so much confidence."
Arsenal boss Arsene Wenger:
"I'm sad for my team as they gave a lot and they played well.
"We should have won this game and I don't know what impact it will have but it is a big blow to lose.
"In every game it is the same - we have fantastic potential but we do not get what we should. That is down to experience and a learning process."
Bolton: Jaaskelainen, Hunt (Giannakopoulos 46), Ben Haim, Meite, Fortune (Campo 43), Nolan, Faye, Speed, Davies, Anelka, Diouf (Vaz Te 83).
Subs Not Used: Al Habsi, Tal.
Booked: Davies, Fortune, Campo.
Goals: Faye 9, Anelka 45, 76.
Arsenal: Lehmann, Eboue, Toure, Senderos, Clichy, Walcott, Fabregas, Silva, Flamini (Julio Baptista 59), Ljungberg (Hleb 73), Adebayor.
Subs Not Used: Almunia, Djourou, Hoyte.
Booked: Ljungberg, Lehmann, Senderos, Toure.
Goals: Silva 45.
Ref: M Dean (Wirral).
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