Ironically it was Bolton who were Charlton's only victims of the season so far when they lost 2-0 to goals from Darren Bent. But it was his namesake Marcus who provided the winning hit for the London side with a well-placed header from a chipped cross from Jimmy Floyd Hasselbaink which was good enough to settle the tie.
Both teams showed their priorities were with the Premiership when they made six changes apiece. Charlton manager Iain Dowie saving some of his star players for Saturday's clash at Newcastle, while Bolton boss Sam Allardyce has never been a great fan of the Carling Cup and he too left out some of his regulars.
Bolton started brightly with Stelios Giannakopoulos missing an early chance, but once Bent had buried his header to give the home side the lead, the visitors seemed more intent on catching their late flight home from Stansted than going through to the next round as Charlton took control of the game.
Hasselbaink twice brought saves out of Ian Walker from well-struck free-kicks.
The home side lost the unlucky Jerome Thomas after 38 minutes when he suffered a whack on his hip and this was only his second game back after a long injury lay-off with a broken foot.
In the second half Bolton got out of their inertia and, sensing that Charlton would be nervous as they had tried to hold on to their lead, pressured the home defence and created their best chance when Kevin Davies saw his effort saved by Charlton goalkeeper Thomas Myhre with his legs.
Davies then headed over and substitute Johann Smith also put a header wide from a good position as the home side held on for the victory.
Charlton boss Iain Dowie has been under pressure following his side's poor results this season, but the crowd of 10,788 got behind both him and their side as they battled to a hard earned victory and will be wishing that they could play the Lancashire outfit more often.
Had Wanderers had their second-half tempo in the first 45 minutes, they may have forced the game into extra-time, but the home side just about deserved to get through.