Stuart Beavon's goal for Wycombe came between strikes from Charlton's Yann Kermorgant and Dale Stephens to give the Addicks victory.
Waddock said: "We played ever so well, but Charlton are where they are for a reason. They take their chances and we don't. That's a credit to them. They deserve to go up as champions. I'm delighted for Chris, his staff and his players.
"But I thought we played ever so well. Over the majority of the season our performances have been like that, but we've not picked up the necessary points and that's why we're in the position we're in."
The Chairboys are now three points from safety with just two games to go and Waddock has targeted victory in both if his side are to stay up this season.
"I've heard the other results, but we needed to get something from this game. We'll keep plugging away and try to get as many points as we can. We have to be really positive and try to win both of them. The way things have been this season who knows."
