In their position five points from safety a draw would have been no use to Charlton, but their chink of light came when Rovers defender Stephane Henchoz body checked substitute Marcus Bent 22 yards from goal with the seconds running out.
Charlton's Moroccan defender Talal El Karkouri stepped up to crash an unstoppable shot past the hitherto immaculate Brad Friedel to send the home supporters, players, and coaching staff into scenes of jubilation.
The battling bottom side certainly deserved the rare sight of three points as they dominated play for long periods but missed some good chances and came up against some fine goalkeeping from Friedel.
Karkouri has been an ever-present in the Charlton side this season and he virtually pushed colleague Andy Reid to one side in his desire to take the free-kick, which finished up in the middle of the net and gave the defender his first goal for 23 months.
Blackburn were always dangerous on the break but the home side stood firm despite having to rearrange their defence after just 27 minutes when the unlucky Djimi Traore, who has only just returned after two months out with a broken leg, limped off with a hamstring strain.
Reed made three changes for Charlton, playing a 4-3-1-2 diamond formation and giving a Premiership debut to winger Lloyd Sam who surprisingly played as a striker alongside Darren Bent.
Sam fired over from close range early on but he can be reasonably pleased with his first full game.
Blackburn failed to produce too many goalscoring opportunities in the first half.
Morten Gamst Pedersen headed into the side-netting and Charlton goalkeeper Scott Carson had to wait until injury time in the first half before making his first meaningful save to deny Benni McCarthy .
Rovers boss Hughes signalled his displeasure at his team's first-half performance by substituting David Bentley and Pedersen at half-time with Tugay and Paul Gallagher.
Darren Bent, who made some great runs for the home side, was twice denied by excellent goalkeeping from Friedel but Hermann Hreidarsson missed the best chance of the came for Charlton, heading over the bar from a clear header following a corner.
Then came the dramatic late finish which will give Charlton hope that they can drag themselves out of the bottom three relegation positions.