Stoke striker Jon Parkin came off the bench to score the winner and put his side top of the Championship table.
Parkin had only been on the pitch for a few minutes before nutmegging Patrick McCarthy in the penalty box and lashing the ball past goalkeeper Nicky Weaver.
Andy Reid had earlier opened the scoring for Charlton with a free-kick.
But Ricardo Fuller equalised in spectacular fashion after controlling the ball with his back to goal and unleashing a fierce shot into the net.
Stoke defender Ryan Shawcross:
"We have started the season very well after a win against Cardiff and now this victory.
"We are flying at the moment with two wins out of two and we are playing with a lot of character and determination.
"Jody Craddock signed for us on Friday without training with us just came into the side and was brilliant for us."
Charlton manager Alan Pardew:
"It is not a disgrace to lose here. There are only seven or eight teams in the division who are as good or better than Stoke at home.
"I thought we were unlucky to lose Yassin Moutaouakil to injury early in the
second half and I think that cost us the game.
"We were beginning to show our quality and I was starting to feel comfortable, but losing Yassin meant we didn't have another natural right-back. We were a bit disorganised and Stoke took advantage of that."
Stoke: Simonsen, Wright (Buxton 33), Craddock, Shawcross, Dickinson, Lawrence (Eustace 90), Matteo, Delap, Cresswell, Sidibe, Fuller (Parkin 74).
Subs Not Used: Hoult, Pulis.
Booked: Buxton, Eustace.
Goals: Fuller 57, Parkin 78.
Charlton: Weaver, Moutaouakil (McCarthy 56), Bougherra, Fortune, Thatcher, Sam (Thomas 46), Ambrose, Semedo, Reid, McLeod (Iwelumo 46), Bent.
Subs Not Used: Randolph, Zheng.
Goals: Reid 55.
Ref: G Laws (Tyne & Wear).