A Ryan Cresswell own goal handed Championship side MK Dons an early lead in a tie which ebbed and flowed as Northampton showed why they have enjoyed such a good season at the head of the League Two promotion race.
Ryan Holmes turned the tie around for the hosts with two goals after half-time but striker Nicky Maynard, summoned from the bench, netted an equaliser on 82 minutes.
It means a replay which is probably not the outcome that either manager wanted but neither side deserved to lose in front of a sell-out Sixfields crowd of 5,878.