Substitute Jon Parkin's 76th minute effort proved to be the difference in this afternoon's entertaining encounter at Glanford Park.
186 Grecians made the long trip and they saw their side create their fair share of chances while at the other end Artur Krysiak made a string of terrific stops to keep the game goalless.
But with 14 minutes to go and both sides pushing for a winner, Krysiak allowed Parkin's hopeful effort to squirm through him and into the back of the net.
It means the Grecians remain eight points from safety with just five games to go.
Paul Tisdale made a raft of changes to the side held 1-1 by Colchester last weekend and opted for a 4-4-2 formation. Jamie Cureton, unavailable for Monday's clash with Orient at The Park due to the terms of his loan deal, partnered Fulham loanee Lauri Dalla Valle upfront for the Grecians, wearing all black.
A four man midfield saw Liam Sercombe and Jake Taylor return to the side and join James Dunne and David Noble. Billy Jones returned at left-back after a spell on the sidelines with Steve Tully at right-back and centre backs Troy Archibald-Henville and Pat Baldwin.
The opening of the match was a little shaky for the Grecians with the home side enjoying a string of corners that Troy and Baldwin did well to repel.
City's first chance of the game came on 14 minutes. After his long throw was headed out of the box Dunne curled in a delicate cross from the right hand side which Dalla Valle met, rising above his marker inside the box, but he headed straight into the grateful arms of Sam Slocombe.
It was the Iron though who had the best chance of the first half on 23 minutes, a corner was sent in and David Murfin leapt inside the box to meet it but the instructive outstretched leg of Artur Krysiak was enough to turn the ball behind and deny what would surely have been the game's opening goal.
And another set-piece two minutes later saw defender Cliff Bryne with his head in his hands. A curling free-kick landed on his head inside the box but Bryne could only nod well wide of Krysiak's goal.
At the other end Cureton's lovely flick looked to have teed up Tully but captain Paul Reid hacked the ball behind and two minutes later Dunne thumped an effort into the crowd.
On 43 minutes Cureton was involved again in a City attack. After a good passing involving Taylor the former Norwich striker was teed up but he snatched at his right footed shot and couldn't test the keeper.
Troy continued to be City's stand out performer at the back with a number of vital blocks and tackles as the large and powerful home side tried their luck before the half-time interval.
It took nine minutes of the second half for Scunthorpe to carve out a chance and what a chance it was. On 54 minutes Andy Barcham made the most of Tully's misplaced pass and from the left-hand touchline he teed up Josh Walker whose right foot screamer thumped off the bar with Krysiak just a relieved spectator.
The hard-working Dalla Valle was then replaced by Richard Logan as City looked to edge the battle with the Scunthorpe backline.
Noble then forced Slocombe into his first big save of the afternoon with a right footed free kick across goal which the keeper needed to be at full strech to stop.
But the resulting corner was cleared, Conor McAleny went on a mazy run, getting the better of Taylor and then Tully, and once inside the box he was denied by a fine save by the feet of Krysiak and when the ball fell to Jimmy Ryan but he couldn't shoot either side of City's Polish keeper.
Ryan then came agonisingly close to the opening goal just seconds later, cutting inside from the left and unleashing a lovely right footed shot across goal that flew off the base of the post and out to safety as this game really sparked into life.
The home support only had to wait another 10 seconds for another chance, Barcham drilling a right footed effort towards goal that the diving Krysiak saved and then Tully had to hack off the line. Amazingly this game was still 0-0 despite bags of chances.
It was City's turn to threaten on 70 minutes, Sercombe unleashing a stunning shot from 30 yards that Slocombe had to tip over his crossbar. Dan Nardiello was then introduced for Sercombe as City prepared to take the resulting corner which came to nothing.
Slocombe was called into action again on 74 minuets from a left-footed Jones free kick that he had to push over the bar.
It was City's keeper in the spotlight though on 76 minutes, this time for all the wrong reasons after a string of superb saves. Sub Jon Parkin had been on the pitch a matter of minutes when he picked up a pass from the left-hand side and tried his luck with an effort from left to right that squirmed through Krysiak and into the back of the net.
Alan Gow was then introduced as City looked to get back into this end to end clash.
Barcham then missed a huge chance to kill the game off, poking wide when put in down the right-hand side.
With four minutes to go Gow tried to take matters in his own hands, going on a lovely run but his left-foot shot deflected wide. But that was the best the Grecians could muster as they failed to score on the road for the 15th time this season.