Rafael Benitez's side conceded two goals in the last three minutes of the first half and it was a nightmare return to the Liverpool side for the Poland international goalkeeper Jerzy Dudek.
He was making his first senior appearance since his Champions League final heroics against AC Milan in May, in place of the suspended Jose Reina.
Dudek had barely been troubled by the Charlton attack for the first 43 minutes of the game until he gave away a controversial penalty when his challenge on Darren Bent was adjudged a foul by rookie Premiership referee Andre Mariner.
Dudek escaped with a yellow card, but failed to stop Bent scoring from the spot for the striker to record his 15th goal of the season.
Jamie Carragher, captain for Liverpool in the absence of the sorely missed Steven Gerrard, was booked for dissent after angrily shaking his fist at the referee at the penalty decision.
Worse was to follow for Liverpool in stoppage time in the first half when poor defending allowed Charlton skipper Luke Young to score a second, firing in from an acute angle; his shot going through Dudek's legs after the visitors' defence had failed to deal with Alexei Smertin's cross.
Liverpool created a few first-half chances, the best one falling to Fernando Morientes, who shot straight at Thomas Myhre in the Charlton goal, and Peter Crouch headed wide.
Charlton's only first-half effort before the goals was a long-range Radostin Kishishev effort.
Not surprisingly Liverpool attacked Charlton with determination at the start of the second half, desperately looking for an early goal to get back into the match.
But Charlton almost put the game completely out of their reach with first Darren Bent rattling the crossbar and then Marcus Bent hitting the post.
On the hour, Robbie Fowler made an emotional return to a Liverpool shirt, but was unable to make any difference to his side's effort to get back into the game.
Liverpool have certainly hit a sticky patch and have now taken just one point from their last four league games.
They have kept just one clean sheet in seven matches and are shot-shy in attack where their multi-million pound strikers are failing to find the net.
Liverpool obviously don't like the London air and have failed to win on any of their last nine visits to the capital.
For Charlton however this was a tremendous and possibly unexpected result, while the upturn in their home form has now seen them keep clean sheets in their last four Premiership matches at The Valley.