The Cumbrians stretched their unbeaten league run to six matches and collected a ninth victory on their travels this season thanks to goals from Karl Hawley, Michael Bridges and Danny Livesey.
It was not as straightforward as the scoreline suggests, as Northampton dominated the first half and should not have been trailing at the break.
As early as the fourth minute Andy Kirk went close with a glancing header and although Chris Billy responded with a venomous drive which flashed just wide, it was the home side who were in control.
The match swung in three action packed minutes. Firstly, Gavin Johnson cracked a tremendous 25 yarder which rebounded back from the underside of the crossbar, before barely a minute later David Hunt saw a screamer whistle over the top.
Incredibly, Carlisle made the most of their narrow escapes by grabbing a 21st minute lead when a back pass by Jason Crowe led to indecision in the home defence, allowing Hawley to nip in for his 24th goal of the season.
The Cobblers went close again when Scott McGleish headed wide, before the same player almost cashed in on a goal kick from Keiren Westwood which held up in the wind, but the striker's effort flew just wide.
Westwood then had to make a brilliant diving save to deny Eoin Jess, and it seemed only a matter of time before the home side levelled.
It was a different story after the break as Carlisle controlled affairs with Hawley twice going close before Bridges crashed in a terrific volley with 16 minutes left, letting fly from 25 yards and catching Lee Harper off his line.
The Northampton goalkeeper was at fault a minute from time when he dropped a corner from Chris Lumsdon and central defender Livesey knocked the ball home from close range.