Reds remain outside the League One relegation zone with four games to go despite suffering only their second defeat in seven games at Glanford Park.
An unfortunate own goal by Ryan Dickson and Paddy Madden’s close range second gave Scunthorpe a 2-0 lead before Izale McLeod pulled one back with his 21st goal of the season with 14 minutes to go.
Reds had four strikers on the pitch at the end but couldn’t conjure up the chance to equalise and they now go to Walsall on Tuesday night looking for a positive result in the battle to stay up.
With Richard Wood returning to Rotherham this week, Dean Saunders made one enforced change to the side which beat Oldham on Easter Monday with Kelly Youga handed a debut in central defence for his first Football League start since April 2013.
Matt Harrold, who returned from his loan at Cambridge United on Friday, was among the subs.
The home side almost made the perfect start. Top scorer Madden beat Dickson on the right and squared the ball to Jordan Clarke whose low drive from 15 yards beat Brian Jensen but Lee Fowler was on the line to block his shot.
Reds settled into the contest and Izale McLeod went close with their first chance on 15 minutes. Ryan Dickson and Gavin Tomlin created the opportunity with a good exchange down the left, McLeod hit Dickson’s pass from 20 yards and keeper Luke Daniels had to tip it over his crossbar.
But it was the hosts who broke the deadlock in fortuitous manner on 19 minutes. Gary McSheffrey robbed Dickson on the right and found Clarke whose shot took a big deflection off Dickson, wrong-footing Jensen who seemed to have the shot covered.
Jensen got fully behind McSheffrey’s 20-yarder as the hosts looked for a second then Isaiah Osbourne tried his luck from distance but his shot was always heading comfortably off target.
The goal was in keeping with a fairly undistinguished first half. Reds had seen plenty of the ball but had rarely troubled Daniels in the Iron goal while at the other end McSheffrey and Madden were a constant threat for the hosts.
Dutchman Kevin van Veen had the first effort of the second period at the end of a decent move when Jensen held his curling effort from the right, although Madden who was hoping to pick up any scraps had strayed offside. Madden then found space on the right for a drive which Jensen blocked for a corner at his near post.
Jensen made another save on 58 minutes, pushing away a fiercely struck effort by Osbourne as Scunthorpe continued look the side likely to score the next goal and it duly arrived on 63 minutes. Dean Morgan headed away a corner but when the ball came back into the six-yard box from the right Madden reacted quickest to give Jensen no chance from close range.
Jensen made a great save two minutes later to prevent the concession of a third goal. McSheffrey found space in the box and aimed for the far corner but the veteran Dane got his angles spot-on and pushed it away for a corner.
Reds responded and Morgan’s snap shot on the turn was blocked by Daniels without the goalkeeper knowing too much about it.
Saunders made two quick changes with Gwion Edwards and Mathias Pogba replacing Dickson and Marvin Elliott as Reds went with three up front for the closing 15 minutes in an effort to salvage something.
And it worked with Reds pulling one back on 76 minutes. Tomlin found Young whose volleyed cross was dummied by Pogba and McLeod ran in unchallenged to slot the ball into the far corner.
The hosts had a great chance to seal victory when McSheffrey weighted a pass into the path of the over-lapping Osbourne, but Jensen was out quickly to block and Edwards cleared the loose ball.
Harrold came on for Lewis Young in the 87th minute, giving Reds four strikers on the pitch, and Scunthorpe broke moments later through van Veen whose powerful shot was beaten away by Jensen.
Reds pumped the ball forward at every opportunity in a frantic but to no avail as the home side held on for a precious win.