It was a vital win for Alan Curbishley's men in the first of three home league games and the result meant they completed the double over their North London rivals having won at White Hart Lane in Martin Jol's as first game as manager.
Charlton's Jerome Thomas, who scored his first goal for the club in that match, put his side ahead after just four minutes of a thrilling encounter with an unstoppable 25-yard shot that flew into the top corner of the net.
The young winger gave Noe Pamarot a roasting before eventually limping off late in the game after suffering a number of heavy tackles.
This was Spurs' third away defeat on the trot, two in the Premiership and one in the FA Cup, but after falling behind to the early goal they created some good chances, the best falling to Frederic Kanoute whose shot was well saved by Dean Kiely and Andy Reid put the rebound over the bar.
Charlton could have increased their lead in the first half when Danny Murphy finished off a 30-yard run with a goalbound shot that was deflected for a corner.
Spurs brought on Jermain Defoe on the hour and played three up front but Charlton battled to hold onto their lead with Spurs' best chance coming from Reid's free-kick which was headed off the line by Shaun Bartlett.
Charlton finally sealed the points five minutes from time when Murphy's free-kick went into the net off the inside of the post despite Paul Robinson's attempt to save.