With the chance to usurp Manchester City and Liverpool ahead of their blockbuster showdown on Sunday, Mikel Arteta's men got off to the perfect start through Declan Rice's opener, but an excruciating Aaron Ramsdale clanger gifted Yoane Wissa the Bees' leveller just before the break.
Arsenal huffed and puffed as the clock ticked down and had to rely on Ramsdale for a couple of crucial interventions, but with a few minutes of normal time remaining, Kai Havertz made himself the hero with a bullet header to spark familiar scenes of Emirates jubilation.
As expected, Ramsdale and Leandro Trossard came into the Arsenal XI in place of the ineligible David Raya and injured Gabriel Martinelli, while Sergio Reguilon was absent for Brentford, who instead called upon Keane Lewis-Potter.
There would be no repeat of Monday's 15-minute four-goal flurry against Sheffield United, as Brentford initially did a good job of keeping the Gunners at arm's length and made a couple of ventures into the hosts' third too.
However, the inevitable Arsenal opener finally arrived in the 19th minute, as Ben White was afforded far too much time in the right half-space to send in an inswinging delivery, which Rice met with a terrific header into the far corner for his sixth league goal of the campaign.
Naturally not satisfied to declare at one, Arsenal immediately resumed their mission for number two and had a sighter of goal in the 24th minute, but Havertz's low strike was straight down Mark Flekken's throat.
The Bees' cause was not helped by an injury to Christian Norgaard, who had tried to soldier on after receiving treatment but ultimately had to cede his place to Mathias Jensen with 34 minutes on the board.
Just one moment later, Jorginho sprayed an exquisite pass through to Havertz, whose blushes were then saved by the offside flag as his dink over Flekken landed the wrong side of the post, but replays showed that he may have timed his run perfectly.
The German then sent a 43rd-minute volley sky-high as Arsenal were frustrated in their attempts to find a second, but Arteta's men would ostensibly enter the break a goal to the good as injury time ticked down.
However, after surviving a couple of howlers in the reverse fixture, there was no hiding place for Ramsdale after a costly calamity in the third additional minute, as the Englishman took too long to clear his lines and was charged down by Wissa, who saw the ball cannon into the net off his outstretched leg.
Ramsdale did manage to partially atone for his horrific blunder 10 minutes into the second half, producing a vital fingertip save to prevent Ivan Toney from scoring an outrageous strike from the left wing, and the kitchen sink was henceforth thrown at the Brentford backline from the men in red.
The Gunners nearly made one of their beloved set-pieces count in the 59th minute, but Gabriel Magalhaes's header was blocked on the line by a combination of Vitaly Janelt and Toney before Flekken managed to gather.
A couple of Arsenal penalty appeals also fell on deaf ears - one for Mads Roerslev's pull-back on Trossard and a second for a Nathan Collins tackle on Havertz - but for all of their slick attacking sequences, they failed to truly trouble Flekken.
In contrast, Brentford defender Collins found himself free in the box to meet Kristoffer Ajer's cross in the 71st minute, but Ramsdale continued his redemption arc with a fine acrobatic stop to tip the ball over.
Brentford had had the better opportunities of the second half up to that point, but Arsenal came ever closer to the coveted second in the 74th minute through Rice, who smacked the upright with a delightful curling strike from 25 yards.
Arsenal's set-piece supremacy was eluding them, but the Gunners were still able to deliver crosses at will from open play, and one such routine led to a late Emirates eruption in the 86th minute.
Conductor Martin Odegaard found the overlapping run of White on the right, and the Englishman once again played playmaker - this time for Havertz, whose bullet header struck the palm of Flekken and flew into the roof of the net.
With the summit in sight, Arsenal did not shy away from trying to score a third and had another strong penalty appeal waved away in injury time - Lewis-Potter appeared to have Gabriel's shirt in a vice-like grip but escaped without punishment - although a one-goal win would nevertheless punch their ticket to first place.
The Gunners now turn their attention to Tuesday's Champions League last-16 second leg with Porto, aiming to overturn a 1-0 deficit from the first fixture, while the Bees travel to relegation-threatened Burnley on Saturday afternoon.