Dean Bowditch then replied for Town, when he turned in a Danny Haynes cross after 25 minutes to bring the game level.
Despite Towns fast youthful side playing well though, there was no end product to their game, with Bowditch and Trotters long-range efforts coming the closest.
Just before half-time Charlton sealed their victory with Alex Varney stabbing the ball home for the Londoners.
*The Reserves will be playing their home matches at Bent Lane or at local non-league grounds next season, so this was the last time fans could watch them at Portman Road, due to fears about the state of the playing surface.
The academy side are set to play a match on the Portman Road pitch on May 1st, with Manchester United the likely opponents. The game will be open to the public, with details are yet to be confirmed.