Cobblers led at half-time at Stadium MK after Manny Monthé headed in Rueben Wyatt’s corner but Charlie Waller and Darragh Burns turned the game around in the space of 10 second half minutes.
Tyreece Simpson briefly levelled from the penalty spot after Wyatt was tripped, but MK Dons made it three wins from three in Southern Group F when Dawson Devoy picked out the top corner with a terrific 25-yard strike.
Brady said: "Obviously we were already out of the competition and you never like to lose, but it was an opportunity to get a lot of players some minutes and that’s how we used it in terms of our shape and how we wanted to play.
"We put a team together and there were a few square pegs in round holes but it was all about getting game-time for those players who need it – that was the most important thing.
"Jon got through a good half-an-hour, which was nice to see, and there were others who really needed some minutes, and it was also good to give the younger players an opportunity to show what they can do, especially Rueben (Wyatt) who started the game.
"It’s great experience for those lads and it’s important for them and for the football club.”
Brady said it was too early to provide any details on the potential injury that forced Ali Koiki to come off in the second half.