After going 1-0 down through Jonathan Leko’s smart finish, Town responded as Pelly-Ruddock Mpanzu found the bottom corner, before Izzy Brown netted his first in a Town shirt as he took a lovely touch before passing it beyond Dillon Phillips.
The result moves the Hatters up to 20th, with 17 points from 18 games.
Jones said: “It’s been a heavy few weeks. I am satisfied more than anything – the result is one thing, but the performance is another. I was really, really satisfied with our performance on Saturday, I have to see beyond results sometimes if we’re making progress and we were, but there comes a point where you’ve just got to get a football result. I said that to the boys tonight.
“We’ve got six months into them in every area, but they’ve been challenged tactically in every single game, there’s been a different set of tactics except in the last two, I picked the same team, I was fortunate enough to be able to do that.
“I asked the boys to take responsibility, they’ve got enough information in them. Charlton changed their shape three times in the game, we adapted quickly, they adapted on the pitch and the players took responsibility for that.”