Josh Murphy's extra-time goal sent MK Dons through to the League Cup third round.
Cardiff had led through Alex Revell's goal in the 53rd minute but 12 minutes from time Carl Baker blasted an equaliser to send the game into extra time.
It was the home side that prevailed when a neat passing move ended with Josh Murphy scing the winner in extra time.
Dons now face Southampton in round 3.
