Jason Crowe grabbed the game's only goal to earn victory for Northampton.
Danny Jackman had a shot saved well by Tim Krul and then cleared off the line by Michael Liddle as the ball spun back towards the goal line.
Richard Keogh wasted a great chance to put Carlisle ahead when he scooped the ball over the bar from three yards.
Crowe headed home the winner from Jackman's free-kick, while Leon Constantine and Andy Holt both hit a the post in the final five minutes.
Northampton: Dunn, Kyle Walker, Davis, Todd, Hughes (Akinfenwa 70), Crowe, Osman, Jackman, Coke, McGleish (Holt 84), Constantine.Subs Not Used: Zieler, Larkin, Gilligan.
Goals: Crowe 63.
Carlisle: Krul, Raven, Livesey, Keogh, Liddle, Taylor, Kavanagh, Bridge-Wilkinson, Jeff Smith (Hackney 66), Bridges (Dobie 66), Graham (Madine 79).Subs Not Used: Williams, Murphy.
Booked: Bridges.
Att: 4,673
Ref: Paul Gibbs (West Midlands).
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