Lisbie, who struggled to score goals in his years as a Charlton player shattered his former team with a brace in the first 29 minutes and the Essex side held on to the three points against a poor Addicks team, whose play-off hopes are beginning to look distinctly dodgy.
Lisbie opened the scoring for the visitors from the penalty spot on 15 minutes after he himself had been brought down by Patrick McCarthy and a mistake by McCarthy allowed the Colchester striker to net his second with an overhead kick on 29 minutes to give the U's a crucial two-goal lead.
McCarthy was substitute by Charlton and went straight to the dressing room and his replacement, Luke Varney, got his side back into the match with a goal right on half-time, converting Lloyd Sam's cross from close range.
With all the second half to get themselves back into the match, Charlton would have been expected to at least get an equaliser against the Colchester side, who have now gone 23 matches without keeping a clean sheet.
However, the home side produced virtually nothing in front of goal until the dying minutes when Zhi Zheng headed wide and substitute Darren Ambrose shot wide as desperate Charlton ran out of time.
This was the home side's fifth defeat at The Valley this season and they were booed off the pitch at the end by their frustrated supporters, but this was an excellent three points for Colchester.