David Ngog climbed off the bench to net a second-half double for Wanderers, with Powell's side dropping back to 14th in the Championship table.
Powell was left to reflect on his side's failure to convert a number of chances, and he insisted the Addicks should not have left the Reebok Stadium empty handed.
"We were disappointed because we grew into the game and created the better chances," he said. "Bolton have obviously come down from the Premier League and that always makes it a difficult game.
"We are good away from home and we got the right balance between attack and defence throughout today.
"In the end, though, we were beaten by a substitute who has a huge pedigree in the game and he has made a huge difference.
"I'm sitting here thinking that we should have won that game but we'll be looking to go into the Christmas period trying to bounce back from a defeat which shouldn't have happened."