It was the Addicks' fourth League defeat at The Valley this season and put a further dent into their play-off and promotion aspirations.
But it was another excellent day for Burnley's recently appointed manager Owen Coyle whom after a draw in his first match at homem had picked up victories at Watford on Tuesday and in today's match.
After their home defeat in midweek to Sheffield United, Charlton made four changes for the game and reverted to a 4-4-2 system, but they were stunned after eight minutes when striker Andy Gray headed home Robbie Blake's free-kick.
You would have thought the home side had learnt their lesson but, five minutes later, from an identical Blake free-kick, Chris McCann was left unmarked to head home the second.
With a mountain to climb, Charlton got back in the game on 36 minutes when skipper Andy Reid volleyed home from Danny Mills' cross, but not before Blake had had another free-kick saved.
Charlton threw everything at Burnley in the second half but could not find that vital equaliser. Reid had a shot well-saved by Gabor Kiraly who made an even better stop to deny Darren Ambrose.
Charlton's hopes of getting anything out of the game ended on 70 minutes when Mills needlessly handballed a Burnley cross to give away a penalty and Gray stepped up to fire home the spot-kick for his 13th goal of the season to make it another bad week for the home side.