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The Yorkshire side now face a nail-biting end to the season to try and avoid the drop - but look set to be docked 10 points next season because of their cash crisis.
The Millers came close to an early lead against their near neighbours, but Gregor Robertson hit the bar.
Only a superb save from Tommy Evans prevented Rotherham grabbing the lead after 15 minutes when he blocked a shot from David Worrell and then Lee Williamson blazed a 20-yard shot wide.
A smart cross from Williamson found Martin Butler but he glanced a header wide, and when John Mullin and Paul Shaw created an opening, Robertson crashed a shot from the edge of the area that beat Evans but rattled the bar.
Scunthorpe goal machine Billy Sharp squeezed off a hurried shot from six yards after 36 minutes, but his effort was wide.
Five minutes before the break Scunthorpe snapped up a goal against the run of play.
Winger Cleveland Taylor, who had been causing Rotherham problems down the right, teased again before drilling in a low cross and Keogh pounced to crash in a low first-time shot.
Moments later it was Taylor again who had the home side back-pedaling with another mazy run ,but this time his carbon copy cross was cut out by Cutler.
Three minutes into the second half Shaw came close to an equaliser, but his shot on the turn from 20 yards was just over and when Mullin found Butler the Rotherham striker slid his shot wide.
A long throw hurled in by Shaun Barker found its way through and Robertson fired his shot over before Butler pulled the ball back and Worrell floated a thoughtful shot just over.
But eight minutes from the end Andy Monkhouse crossed low from the left and Hoskins, who had arrived three minutes earlier from the bench, drilled in the equaliser.