They did it the hard way, coming from behind after Andy Kirk had lobbed the Cobblers into a fourth minute lead with his fourth goal in four matches since signing from Boston.
But Scunthorpe turned the match on its head in the next 17 minutes. They equalised with Paul Hayes' 19th goal of the season, the striker ending a recent barren spell to cash in on a collective hash by the home defence to prod the ball past Lee Harper.
Scunthorpe went ahead in the 21st minute when the home side lost possession in midfield and, after the ball was played out to the right, Richard Kell timed his run to the near post to perfection to bury a cross from Matthew Sparrow.
Northampton created too few opportunities, although they could consider themselves unlucky early on when Charlie Hearn's shot was tipped onto the crossbar by Paul Musselwhite, while late in the game a Josh Low shot was blocked by team-mate Kirk when it appeared destined for the corner.
Scunthorpe could have extender their lead in the run-up to half-time with a bobbling shot from Hayes going wide in the 34th minute while in first-half injury time, Hayes teed up Ian Baraclough only for the midfield player to direct his 15-yard shot over the crossbar.
The second half was largely devoid of chances at both ends, although Sparrow brought out the best in home keeper Harper just after the restart when he unleashed a fierce volley only to see the Cobblers keeper parry the ball away.
Harper then needed to be alert to deal with a 25-yard effort from Kell.
Northampton's only comfort was that results elsewhere still leave the fourth play-off place wide open.