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Mark McCammon gave The Bee's the lead when he headed home from close range on 37 minutes following a cross from debutant Mickael Antonie-Curier.
However, with 6 minutes left on the clock Joe Keith grabbed a vital equaliser for Phil Parkinson's side from the penalty spot after Scott Marshall had handled in the box.
The result see's Brentford leapfrog Wycombe Wanderers and move go into 12th place, while Colchester go level with Chesterfield on points, and climb above The Spireites on goal difference and go 16th in Division 2.