The match exploded on 29 minutes when Charlton defender Hermann Hreidarsson was sent off after being given a straight red card by referee Mike Dean for elbowing Kevin Davies in the face.
Then in the second half trailing to a Darren Bent penalty, which had given the 10 men the lead, Bolton had Davies himself sent off for exactly the same offence on Amady Faye.
Bolton had missed a penalty when Charlton had 10 men and they had 11 as El Hadji Diouf saw his spot-kick brilliantly saved by Charlton's on-loan goalkeeper Scott Carson, who dived to his right to turn the ball away. Diouf himself had been fouled in what looked a fairly innocuous tackle.
The home side were then awarded a penalty themselves when Darren Bent was fouled by Tal Ben-Haim and the England striker fired home his second spot-kick of the season.
Hreidarsson's sending off was Charlton's second dismissal in three matches, Djimi Traore having been dismissed at West Ham on the opening day of the season, but he returned for this match to make his home debut along with another new signing Andy Reid, who looked impressive in the home side's midfield.
Bolton were looking for their fourth successive victory in the Premiership against Charlton at The Valley and, after the sending off, should have taken the lead by the interval.
Stelios Giannakopoulos missed two gilt-edged chances to put his side in front; firstly when clean through with only Carson to beat, he delayed his shot so long that a defender was able to get back and clear the ball for a corner. He then planted a header wide of the post.
Charlton's best effort came from a move which saw them have a goal disallowed.
Darren Ambrose's shot was well saved by Jussi Jaaskelainen, the ball came out to Darren Bent but his shot was cleared off the line. Ambrose put the rebound into the net but was adjudged to be offside.
Charlton almost took a shock lead straight after the break when Talal El Karkouri headed just over the bar from a free kick.
Then came Diouf's penalty miss which, in the end, was to turn the game on its head.
Bent slotted home Charlton's spot-kick and then made sure that Charlton would get their first points of the season when he scored the second goal after goalkeeper Carson's long clearance had been headed on by Jimmy-Floyd Hasselbaink. Bent got behind the defender to turn the ball into the net.
Bolton's record £8million signing Nicholas Anelka watched the match from the dugout and is likely to make his debut in Bolton's next match in two weeks' time.