Dean Leacock's tap in on 81 minutes sealed victory for the hosts in a game which really should have been wrapped up by United long before then.
The away side were dominant but missed a number of chances to secure what would have been a vital away win.
On nine minutes, Sodje was next to come close as he was played through down the right side of the area by Duffy and he saw his low drive tipped away for a corner by
The hosts were next to have a shot two minutes later when Jeff Hughes' curling shot cleared the crossbar.
Then, Mirfin headed wide from the subsequent set-piece as Scunthorpe looked to keep up the early pressure.
Scunthorpe were quick out of the blocks on a sunny day at Meadow Lane and came close when Reid found space at the back post in the second minute following a Newey free-kick but his effort was deflected wide for a corner.
The substitutes were James Severn, Josh Walker, Mike Grella, Barcham, Connor Jennings, Niall Canavan and James Alabi.
The midfield consisted of Mark Duffy, Michael Collins, Jimmy Ryan and Forde, while Akpo Sodje and Karl Hawley led the attack.
Eirik Holmen Johansen started in goal, with Eddie Nolan, David Mirfin, Paul Reid and Tom Newey forming the defence.
On-loan winger Anthony Forde came into the starting eleven for his debut in place of Andy Barcham.
The Iron entered the game making one change from the side beaten by Coventry City a week earlier. It w
Bialkowski. as an opening half which Scunthorpe dominated as they pressed forward with purpose. Hawley almost got on the end of Newey's cross as the visitors threatened to take the lead.
Reid then narrowly failed to get on the end of a Sodje flick-on folliowing Ryan's free-kick as the pressure continued.
Bialkowski then did well to claw away Duffy's free-kick before Sodje could get on the end of it. Next to come close was Hawley, who fooled a defender and cut inside before dragging the ball onto his left foot and seeing it deflected behind for a corner.
The hosts had a great chance on 37 minutes as Alan Sheehan's free-kick found the head of Neal Bishop, who drew an excellent stop from Johansen, who tipped the ball around the post.
Then Alan Judge glanced a header slightly wide prior to Yoann Arquin then sending a header wide unmarked the hosts began to threaten.
Arquin then soon after volleyed over the crossbar from 20 yards for County.
Just before the break, Hawley came close as he held off a challenge and fired wide as an even first half ended all square.
The first chance of the second period arrived on 48 minutes when Sodje tried to hook an effort over the goalkeeper when he chased a hopeful throughball.
There was a substitution five minutes after the break as Reid was replaced by Canavan with what presumably was a knock.
On 60 minutes, Hawley had the chance of the game so far when he drove forward and beat his man before chipping the ball over
He had an even better chance two minutes later when Sodje capitalised on a defensive mistake and and squared the ball across to the frontman, who fired wide with the goal gaping.
Bialkowski and just wide of the goal.
Hawley again was played through by Ryan on 64 minutes but, in a rush to beat Bialkowski to the loose ball, clipped his effort wide from the edge of the area.
After this spell of Iron dominance, the hosts started to come back into the game and came close when Leacock headed over the crossbar from an Alan Sheehan corner.
Then Judge saw his right-footed effort go well wide of goal four minutes later.
Scunthorpe made a change 15 minutes from time as Barcham replaced Forde.
However, after some more United pressure, it was the hosts who went ahead when Leacock struck from close range - connecting with Haydn Hollis' back-post effort to guide home from five yards.
Scunthorpe tried to find an equaliser and Hawley came close again moments after the goal, arrowing a header just wide of the post from 12 yards.
As the clock ran down there were some last minute nerves from the home defence as Sodje very nearly capitalised but saw the ball cleared for a corner.
There were three minutes of time added on but Scunthorpe, who are next in action when they host league leaders Doncaster next Saturday, couldn't find the elusive equaliser.
Carl Boyeson. Referee:
Severn, Walker, Grella, Jennings, Alabi. Substitutes not used:
Johansen, Nolan, Mirfin, Reid (Canavan, 50), Newey, Duffy, Collins, Ryan, Forde (Barcham, 75), Hawley, Sodje. Scunthorpe United:
Spiess, Smith, Bencherif, Thompson. Substitutes not used:
Bialkowski, Liddle, Hollis, Leacock, Sheehan, Hughes, Judge, Bishop, Boucaud (Tempest, 83), Arquin (Zoko, 66), Showunmi (Waite, 90). TEAM LINE-UPS
Attendance: 4,634 (402 away).