First-half goals from Gary Alexander and Toumani Diagouraga gave the Bees breathing space, but Scott Wagstaff ensured a nail-biting finale for the Bees with a stinging volley 16 minutes from time.
Brentford dominated the first half and it was no surprise when Alexander latched on to a loose ball in a box to rifle home into the roof of the net.
Thierry Racon flashed a rare Addicks effort past the upright before Diagouraga made it two-nil to Brentford just after half an hour following a flowing move with a curling drive from the edge of the box.
Veteran striker Nicky Forster tested Charlton goalkeeper Rob Elliot with a low drive just before the break before the game swung in favour of the visitors after the interval.
Pawel Abbott missed two gilt-edged chances to haul his side back into it before Kyel Reid slipped past Michael Spillane to cross for Wagstaff to smash a volley inside the near post. Addicks substitute Akpo Sodje forced a late double save from Bees' goalkeeper Ben Hamer, but the home side held on.