Aaron Amadi-Holloway's goal after 51 minutes secured the win for the Bluebirds.
Barrow move up to 20th, ten points clear of the relegation zone, while Northampton stay fifth, two points off the automatic promotion places.
Story of the match
After a scrappy opening five minutes, Barrow goalkeeper Paul Farman had his heart in his mouth when some good pressing from Josh Eppiah forced Farman into an error which the hosts weren't able to punish.
Northampton created the first real chance of the game on 15 minutes when Aaron McGowan crossed in from the right to pick out an unmarked Mitch Pinnock who took a good touch and saw his shot fly wide of Farman's post.
Barrow then began to have the better of the play without creating any clearcut chances.
The hosts came closer to taking the lead just before the half-hour mark when Ali Koiki crossed to find Paul Lewis at the near post who headed wide.
Northampton began to test the Barrow shot-stopper Farman moments later when he spilt an effort hit by Pinnock from range, Farman managed to hold on to a low, driven Sam Hoskins effort shortly after.
The final 15 minutes of the first half failed to entertain as the sides went in goalless at halftime.
Half time: Northampton Town 0-0 Barrow.
Barrow started well in the second half and took the lead six minutes after the break when Amadi-Holloway arrived at the back post unmarked to head home John Rooney's cross from the left.
The visitors almost doubled their lead when Ollie Banks' free-kick from range was saved down low by Northampton goalkeeper Liam Roberts.
The Cobblers came close to equalising seven minutes later when the ball fell to Lewis on the edge of the penalty area whose volley was comfortably saved by Farman.
Northampton continued to press for the leveller when Koiki crossed deep to find McGowan at the back stick who headed across goal to find substitute Danny Rose, his header was comfortably saved by Farman.
Northampton pushed for the equaliser but Barrow did well to shut out their promotion-chasing opponents who couldn't find a way through.
Full time: Northampton Town 0-1 Barrow.
Takeaways from the game
Gameplan well executed by the Bluebirds
It wasn't a pretty display from Barrow, or Northampton for that matter, but what they did do was bring Northampton down to their level.
The visitors kept the ball well in the first half and frustrated Northampton who were not at all at the races.
Barrow arrived at Sixfields to grab a goal and defend it, which is exactly what they did in the second half.
Once they took the lead through Amadi-Holloway their excellent defensive organisation and game management, particularly in the second half, won them the three points on Tuesday night.
Barrow fans were delighted when they resigned John Rooney on Sunday and he showed them why on Tuesday night.
Rooney's creative spark was clear for all to see and his pinpoint cross to Amadi-Holloway for the goal was crucial in them securing the win.
Along with Ollie Banks, Rooney will certainly provide creativity and goals which could ensure the Bluebirds’ survival this season.