Two goals in six second-half minutes gave Scunthorpe a 2-0 win and the edge in the Northern Area Final against Rotherham.
Winger Martyn Woolford opened the scoring on the hour when he beat goalkeeper Andy Warrington from close range after a well-worked move that split open the Millers defence.
Woolford almost added another but his well-struck effort was brilliantly turned away by Warrington.
However, from the resulting corner Scunthorpe did make it 2-0 when centre-back Krystian Pearce rose at the far post to head home.
Midfielder Matthew Sparrow went close to adding a third for the Iron but Warrington again made a good save.
League Two basement club Luton produced a highly creditable 0-0 draw to put their Southern Area Final against Brighton in the balance going into the second leg at Kenilworth Road.
Mick Harford's side - still stuck on zero after starting the season with a 30-point deduction - battled gamely throughout against League One strugglers Brighton.
Recalled Seagulls striker Jake Robinson failed to connect from a good position early on and also forced Luton goalkeeper Conrad Logan to parry his shot shortly after the break.
Luton keeper Logan came to his side's rescue shortly after the break as he parried a goalbound strike from Robinson.
Luton rarely threatened in front of goal, although Asa Hall directed a header wide at the far post following Rossi Jarvis' free-kick 14 minutes from time.