The key action of the game came just after half-time when the Cobblers, backed by over 6,000 supporters, thought they had opened the scoring only for MK Dons to then be awarded a penalty at the other end.
Ben Reeves netted the spot-kick and Josh Murphy made the scoreline more comfortable for the Championship side on the hour mark and a second penalty, again controversially awarded, sealed the scoreline in the final minutes although Chris Wilder's men kept going until the last whistle.
It is the Dons who will go on to meet Chelsea in the Fourth Round, live on the BBC, but although that would have been a big date for Northampton there will still be plenty of occasions to savour for Town supporters between now and the end of the season if they can continue their excellent League Two form.
Morecambe are the visitors to Sixfields this Saturday.