Daniel Nardiello sparked the Millers` recovery after their recent disappointing home form with a goal from the penalty spot five minutes before the break.
But two goals in three minutes set the seal on Rotherham's performance. Ben Pringle doubled Rotherham's advantage after 75 minutes and David Noble made sure the points were secured minutes later.
Clarke Carlisle's injury time header for Northampton was no more than a consolation.
"We didn't deserve anything out of the game," he said. "I think for the first time this season we got out-worked, and I very rarely say that about our players.
"Rotherham worked harder than we did, and if you don't work hard then you get turned over and that's what happened.
"When a team is under a bit of pressure they send us along because we seem to get them up again, and I don't know why that is because we are better than that, far better than that, but we can't be good every weekend.
"We knew what Rotherham do, we knew how they play and we didn't get our normal game going. We didn't get hold of the ball, we didn't make good decisions they hurried and harried and you have to give credit to them and we didn't deal with it very well."
"You have to give credit to the opposition, they were their points today and they deserved them," Boothroyd added.
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- Ben Pringle