After going three goals down on 62 minutes, Town stirred themselves with a fight back that came so close to securing a point.
Goals from Ivan Toney on 79 and Stewart Murdoch in the 89th minute were just reward for the Cobblers efforts but manager Chris Wilder felt the comeback 'papered over the cracks' in his team and confirmed they would be training on Sunday.
Northampton are 16th in League 2. The attendance was 4318.