Goals from Donaldson and Miller sealed all three points for Crewe Alexandra at Gresty Road as Ian Sampson's side missed out on a chance to move up a congested League Two table.
Northampton now lie 19th in the division, 5 points above the relegation zone and will look to ease away from the bottom two when they host Lincoln City at Sixfields on Monday.
Reaction to follow on Cobblers Mad.