An 87th minute penalty by skipper Andrew Crosby finally secured all three points for the home side in a game they dominated from start to finish.
It provided a successful start for caretaker manager Nigel Adkins in his first league game in charge.
Scunthorpe tore into Northampton from the very first whistle and it was only a string of fine saves from goalkeeper Mark Bunn that kept the visitors in contention.
Twice in the opening minutes he did well to keep out efforts from left winger Ian Morris. He also went full-length to turn away a close-range shot from Andy Keogh.
When he was beaten by leading marksman Billy Sharp, midfield man Ian Taylor was on hand to make a goalline clearance.
Northampton failed to muster a single effort on goal in the opening 45 minutes.
It was a similar pattern in the second half in which goalkeeper Bunn was lucky to escape with just a yellow card when he raced out of his box to clatter into winger Cleveland Taylor.
Sharp and Keogh were always a threat to the visitors' defence, while the pace of Cleveland Taylor created plenty of openings.
Cleveland Taylor himself was unlucky with an angled drive that thundered back off a post.
Time seemed to be running out for Scunthorpe when they earned an 85th minute penalty when a ball into the box from Keogh was handled by Northampton centre-back Sean Dyche.
It enabled Crosby to step up and score from the spot for Scunthorpe who have now lost only once in their last 11 league games.
Yet Northampton might have snatched an equaliser right at the death when Ian Taylor burst through the middle only to be denied by a last-ditch challenge from Marcus Williams.