Mikel Merino headed home a cross from Ben White in the 11th minute for the opening goal. They were two of the backups starting at Emirates Stadium for Arsenal, who were without the likes of injured first-choice centre backs Gabriel Magalhaes and William Saliba, and began with stars Bukayo Saka, Jurrien Timber and Eberechi Eze on the bench.
Saka came on as a substitute and added the second in added time, his shot crawling over the line after being parried by Brentford goalkeeper Caoimhin Kelleher.
Arsenal's squad depth is such this season that Mikel Arteta's team can withstand so many absences and still stay strong in the title race as the Gunners seek a first league championship since 2004.
In other matches on Wednesday night, Aston Villa came from 2-0 down to win 4-3 at Brighton & Hove Albion, who dropped one place to seventh.
Ollie Watkins scored twice for the Villains, who posted a fourth-straight victory to go above Chelsea into third.
Just days after holding London rivals Arsenal to a draw, Enzo Maresca's Blues suffered a shock 3-1 loss at Leeds United to lift the hosts out of the relegation zone.
At Anfield, Sunderland's amazing return to the top flight continued by holding defending champions Liverpool to a 1-1 draw.
Both goals came in the second half, with efforts from Chemsdine Talbi and Florian Wirtz finding their way into the net via deflections.
The Black Cats dropped to sixth and the Reds remain in eighth.
Crystal Palace went fifth thanks to that result and their 1-0 away victory over Burnley. Colombia wing back Daniel Munoz' with the 44th-minute goal.
Last-placed Wolverhampton remain without a win this campaign after losing 1-0 at home to Nottingham Forest. After 14 rounds, Wolves have just two points and are already 12 points from safety.
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