Midfielder David Hunt drove the Bees ahead in the 13th minute with a shot from 20 yards after Clive Platt had headed away Kevin O’Connor’s free-kick.
And Brentford doubled their lead four minutes later through defender Leon Legge, who headed home unchallenged from Hunt’s corner.
But Colchester reduced the deficit just after the half hour through Hunt, who put through his own net from six yards from Ian Henderson’s short cross.
And on the stroke of half-time, Anthony Wordsworth headed in Prutton’s corner at the far post, despite the best efforts of Ben Strevens on the line.
Brentford restored their lead 12 minutes into the second half through Charlie MacDonald, who squeezed a low shot past Ben Williams – but Prutton converted Kevin Lisbie’s low cross from close range with 14 minutes remaining to level the scores.