Paul Hayes grabbed his 11th goal of the season to give the visitors the edge in the first half and, despite a second-half fightback by the home side, The Iron hung on.
Scunthorpe's breakthrough came in stoppage time at the end of the first half when Nyron Nosworthy was left floundering as Donal McDermott breezed past him down the right.
McDermott cut back a neat ball into the path of striker Hayes who struck a low shot out of Steve Simonsen's reach.
It left the home side cursing after they had gone close with a hat-trick of early chances that should have seen them edge in front.
Darius Henderson produced a super cross and Richard Cresswelll should have hit the target but aimed his header over the top.
And when Paul Connelly struck a stinging shot through a crowd of players, David Mirfin blocked and then cleared the danger.
Mark Yeates should have given the Sheffield club the lead when he had a clear header from a Cresswell cross but it was high over the bar.
Yeates went close again with a free-kick that he curled over the Scunthorpe wall but it drifted over the bar.
On the break Scunthorpe menaced and a free-kick from Sam Togwell forced Simonsen to smother at the second attempt.
The visitors could have gone in front when a slip by Kyle Bartley let in Garrry Thompson and his shot almost squirmed under the keeper moments before the goal.
Ten minutes into the second half, Yeates came within a whisker of the equaliser when he struck a super free-kick but Joe Murphy matched it with a stunning save.
Stephen Quinn fired wide, Bartley headed over from Yeates' free-kick and a Henderson header went over after a Glen Little cross.
And seconds from the end Murphy saved again when Bartley headed Little's cross towards goal.