All the action came in the second half after a stalemate opening 45 minutes in which neither side managed a shot on target.
Relegation-threatened Northampton worked hard to frustrate the home side in the early stages.
Scunthorpe finally broke the deadlock in the 52nd minute when centre-back Niall Canavan was on hand at the far post to turn home an inswinging corner from Andy Dawson.
It was his fourth goal of the season and looked to have set his side on the way to victory.
That looked even more likely six minutes later when the visitors were reduced to 10 men when skipper Ricky Ravenhill was sent off for a second yellow card.
But improving Northampton, who had taken 10 points from their previous five games, showed their battling qualities with an equaliser in the 65th minute when centre-back Zander Diamond headed home from a free-kick by Darren Carter.
Scunthorpe pressed forward again to try and repair the damage and keeper Matt Duke was forced to rescue the visitors with a point-blank save from a header by Paddy Madden.
But Northampton refused to let their grip go on a point which boosts their hopes of avoiding the drop.