Kelvin Langmead's last-gasp winner for Northampton ensured a losing start for Gary Rowett in his first game as Burton caretaker manager.
The Brewers looked set to earn a point and end a run of six straight defeats, a statistic which at the weekend.
But Langmead scored in stoppage time from a goalmouth scramble to snatch victory for the visitors.
Burton went close through Greg Pearson and substitute Jimmy Phillips.
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Burton Albion caretaker boss Gary Rowett told BBC Radio Derby:
"It was a bit of a killer at the end. I'm not sure they created that much, other than their set-pieces, and they obviously cause you a problem with them. They're good at it, they work at it, they've got the bodies in there to do it.
"I'm just so disappointed that for 89 minutes we've headed everything away - we've put our bodies on the line. They've given me everything I had asked for and yet they score just at the end, so it's very disappointing.
"I think we had five or six half-chances when balls flashed across the box, so I was really pleased with that."
Northampton Town manager Aidy Boothroyd told BBC Radio Northampton:
"We've ground out a win. I didn't think they could handle our set-plays for long periods, but I didn't think we used our extra man in midfield very well for long periods.
"In the end, I went for it. I'm delighted because it puts a bit of distance between us (and the relegation zone).
"The dressing room is very, very happy and we feel we deserve it.
"There's a fine line between complacency and confidence, and I thought we perhaps stepped over it on Saturday, but tonight it was back to basics. I wanted to come away with a clean sheet."