Trophy exit for Millers
A 30-yard strike from Conor McLaughlin 20 minutes from time sentenced them to a 2-1 defeat in the northern area semi-final.
It was a mistake from goalkeeper Adam Collin, letting Jeff Hughes' close-range shot squirm through his legs, which handed the home side a 19th minute lead.
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Hide AdKieran Agard forced a save from Scott Davies and Craig Morgan flashed a header just over as Rotherham tried to find a way back.
The game opened up in the second half and Alex Revell clobbered the outside of the post soon after the restart before loan man Nouha Dicko tucked home the equaliser from close range on 55 minutes.
The goal sparked Fleetwood back into life and although Collin did well to foil Antoni Sarcevic, he couldn't keep out McLauglin's measured strike.
Davies pulled off super save to deny both Lee Frecklington and James Tavernier in the dying minutes.
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Hide AdFleetwood: Davies, McLaughlin, Taylor, Roberts, Pond, Evans (Cresswell 89), Hughes, Sarcevic, Schumacher, Blair (Brown 78), Tyson (Carr 76)
Millers: Collin, Bradley, Tavernier, Morgan, Arnason, Agard, Pringle, Frecklington, Vuckic (Davis 79), Revell, Dicko
Referee: Scott Duncan (Northumberland)
Attendance: 2,244