And it was the sort of result that suggests Arsenal have the character within their squad to maintain their push for the title.
The result is the second straight defeat of Owen Coyle's tenure as Bolton manager and his team remain in the bottom three.
But the Wanderers boss can regard his side as slightly unfortunate not to have taken something from the game, particularly as his side should have been awarded a foul in the build-up to Arsenal's equaliser.
Having watched Fabregas pull the strings on Sunday, Coyle tried to close down the space available to Arsenal's mercurial Spaniard by bringing in Mark Davies for Ivan Klasnic and playing five in midfield.
Coyle incensed by Gallas challenge
That left striker Kevin Davies with the arduous task of playing a lone role in attack, but he quickly had an impact on the match as he contributed to Bolton's early goal.
Arsenal wasted several opportunities to clear the ball, including one skewed effort from the returning Gael Clichy, and Kevin Davies eventually headed into the path of Cahill, who struck the ball crisply beyond Almunia.
The goal gave Bolton plenty of incentive to keep out their opponents but the home team dominated possession and created numerous openings.
Jussi Jaaskelainen saved a low close-range effort from Fabregas after a crisp move involving Eduardo and Arshavin had carved open the Bolton defence, while the two players involved in the build up both narrowly missed with subsequent efforts.
But for all Arsenal's domination it took Almunia's brilliant one-handed save low to his right to keep out Taylor's clever free-kick.
And just before the half-hour mark, Taylor did double Bolton's lead, his crisp penalty just eluding Almunia's dive after Denilson, back in place of Craig Eastmond, clearly fouled Chung-Yong Lee.
Bolton's plan was working but Arsenal continued to threaten and Jaaskelainen denied Eduardo while Kevin Davies headed against his own crossbar as he tried to clear a free-kick.
Wenger responds to Coyle's criticism of Gallas
Arsenal's pressure eventually told when Rosicky created a yard of space before unleashing a thunderous strike and the home team almost restored parity before the break but Jaaskelainen saved well from Fabregas.
The Gunners did equalise shortly after the restart but it was a goal mired in controversy.
Fabregas's finish was awesome, the skipper collecting the ball inside the Bolton area and eluding the visiting defence before slotting the ball between Jaaskelainen's legs from a tight angle.
However, in the build-up to the goal Gallas challenged for the ball with Mark Davies - the Arsenal defender was late and caught his opponent on the ankle in what was an awful looking challenge.
Play was allowed to continue and Gallas retrieved the ball to start the sequence that led to the goal, while Davies was eventually stretchered from the field.
Vermaelen struck with his vicious half-volley from eight yards after Bolton had failed to clear a corner.
The traffic was all one way but a reasonable opportunity fell to Tamir Cohen only for the midfielder to scuff his effort from 20 yards.
The final goal belonged to Arshavin as he exchanged passes with Eduardo - and it was a goal that took Arsenal to the top of the table.
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