The Londoners had started the day ten points adrift of safety knowing that they had to win the majority of their 12 remaining games to have any chance of survival, but this defeat could have put the final nail in their coffin and they have now only won two leagues games out of 25.
Doncaster had dragged themselves away from danger with an impressive run which has seen them lose only once in 11 matches and after soaking up Charlton's pressure in the first half, they took control of the game after the break despite the home side's efforts to squeeze a point from the match.
Charlton had much the better of the play in the first half and went close to opening the scoring when Tom Soares saw his header rebound off the crossbar.
Charlton's 17-year-old midfielder Jonjo Shelvey, who signed his first professional contract this week, shot on sight of goal but was unable to hit the target.
Doncaster produced very little as an attacking force in the first 45 minutes, but they took the lead four minutes after the break when James Coppinger cut in from the left to score after a clever back-heel by Richie Wellens had set him up.
Charlton dragged themselves back into the match when Nicky Bailey volleyed home from the edge of the penalty area in the 73rd minute.
But three minutes later, Charlton's hopes were shattered when Bailey turned villain and brought down Wellens in the penalty box and Brian Stock converted the spot-kick to give the visitors three points.