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Charlton ended their 13-game winless streak and moved six points clear of the Championship relegation zone in the process.
Brentford came into the game in the play-off places, but with the future of their manager Sam Warburton in doubt - his position would not have been helped by the 3-0 reverse.
Charlton took the lead in 27th minute when Johann Berg Gudmundsson latched onto Igor Vetokele's pass and fired into the top corner.
Vetokele then added a second after the break, racing onto Tony Watt's pass and slotting home.
Frederic Bulot completed the win in the final minute, running clear to score after a mistake from Brentford's Harlee Dean.
The result moves Charlton up two places to 18th.