Initially Scunthorpe found the Cobblers difficult to break down as they strung five men across the back, although they did set the early pace with Matt Sparrow and Andy Keogh linking well on the left.
Most of the visitors thrust came down the right were Josh Low was causing problems with his pace and, in his opening attack, Marc Richards drove straight at home keeper Paul Musselwhite.
That summed up their entire attacking threat and it was the Iron who took up most of the running, with Nathan Stanton getting forward to provide Paul Hayes with a header which flashed over the bar.
Midfielder Ian Baraclough then tested Town shot-stopper Lee Harper with a fine shot which he turned over the bar one-handed, before Cleveland Taylor set up Sparrow, who could only direct his header wide.
Scunthorpe broke the deadlock two minutes from the break when Luke Chambers could only help on a flick from Hayes to Keogh, who turned swiftly to turn the ball home.
Northampton started the second half more brightly and both Tom Youngs and Low were not far off target.
However, they lost concentration allowing Scunthorpe to regain the initiative, with Keogh and Baraclough going close.
The pressure eventually told and Scunthorpe consolidated their lead in the 73rd minute when Andy Crosby converted from the spot after Chris Willmott was harshly penalised for a foul on Hayes.
Cobblers boss Colin Calderwood then incurred the wrath of the officials and was sent to the stand after throwing a water bottle down in anger.
The visitors had a chance to reduce the arrears in the final minute when Richard Kell brought down Eric Sabin, but Scott McGleish's spot-kick cannoned off the post to safety.