The Bees, who knocked the Addicks out of the competition last year, got off to a dream start by taking the lead inside two minutes.
David Clarkson's initial shot was parried by Addicks keeper John Sullivan but the loose ball fell to Blair Adams, who fired a low shot into an empty net.
The Bees doubled their advantage in the 24th minute when they were awarded a penalty following a clumsy challenge by Mikel Alonso on Toumani Diagouraga, with Kevin O'Connor stepping up to smash home the spot kick.
Adams came close seven minutes after the restart when he ran half the length of the pitch before unleashing a 25-yard shot which went just wide of the post.
But Brentford didn't have long to wait until their third of the evening arrived on the hour when Diagouraga shot past Sullivan from 10 yards.