Charlton sealed promotion to the Championship when Bradley Wright-Phillips prodded home his 22nd goal of the season to secure victory.
Carlisle remain in the hunt for a play-off place but are a point behind but do have a game in hand.
The hosts had the better of the game with Liam Noble hitting the post while Jordan Cook also went close.
Adam Collin saved from Wright-Phillips, who later grabbed the winning goal.
VIEWS FROM THE DRESSING ROOM
Carlisle United manager Greg Abbott tells BBC Radio Cumbria:
"I feel sorry for our players today, everything that we haven't got and everything Charlton have got - resources win the day.
"Our board and our fans should be grateful for that group of players.
"I don't like seeing them celebrate, I can't wait to get away from here, there's an enviousness and a jealousness. I'm so pleased for Chris and his players, don't get me wrong, but I wanted to be out there, I want part of that."
Charlton manager Chris Powell told BBC London 94.9:
"Its been a long old season, but I am so proud for everyone connected with Charlton.
"We have worked ever so hard for this. Myself and all my staff, the players and all the supporters have been richly rewarded today.
"I put my full trust in all of them this year and everyone has played their part, no matter how big or small.
"It's a big moment for us, in the re-birth of the club we have had it tough but its been a real team effort and a club effort to get this."