Martyn Woolford and Krystian Pearce scored second-half goals to put Scunthorpe in charge of the Johnstone's Paint Trophy northern final.
Woolford opened the scoring on the hour beating goalkeeper Andy Warrington from close range after a well-worked move that split open the Millers defence.
Scunthorpe made it 2-0 when centre-back Krystian Pearce rose at the far post to head home from a corner.
Rotherham nearly hit back late on but Ian Sharps dragged his shot wide.
Rotherham: Warrington, Tonge, Fenton, Sharps, Nicholas, Jason Taylor (Danny Harrison 78), Hudson, Cummins, Green, Reid (Burchill 73), Broughton. Subs Not Used: Cann, Joseph, Ryan Taylor.
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