Alex McDonald's excellent free-kick gave Burton Albion all three points, netting five minutes from time and just five minutes after Ryan Cresswell had hauled Northampton level.
Town manager Chris Wilder said afterwards: "In the second half, they made it difficult for us, sitting behind the ball and sitting deep," and that was a verdict his opposite number Gary Rowett agreed with.
"I thought we worked ever so hard to restrict Northampton to very few chances."
Town visit Cheltenham this Saturday with their hosts looking for a first league win since the end of August.
They took the lead just after half-time at Shrewsbury this weekend but three quick goals had manager Mark Yates lamenting afterwards that his side 'pressed the self-destruct button' with their defending.