The Millers followed the way of League One rivals and fellow Football League Trophy winners Tranmere Rovers, Carlisle United and Crewe Alexandra out of the competition at the hands of the Cod Army as the Lancastrians moved to within two games of a final at the home of football.
That it took something special to win the tie – a screaming long-ranger from right-back Conor McLaughlin on 70 minutes – will have afforded no consolation to the Millers, who copped a cup exit to Red Rose opponents for the second time in four days.
It was the Irishman’s first-ever goal in professional football as the smallest town to have a team in the Football League moved within sight of an appearance on the grandest stage possible.
While the winner was spectacular, the hosts’ opener on 15 minutes was far from it, with goalkeeper Adam Collin producing a real blooper to present Jeff Hughes with an early Christmas present.
Loanee Nouha Dicko, on his return to West Lancashire, restored parity 10 minutes into the second-half for the Millers, who won the competition, then known as the Auto Windscreens Shield, back in 1996.
But it was to prove Fleetwood’s night, despite a frenzied finale which saw home goalkeeper Scott Davies produce blinding saves to deny Lee Frecklington and James Tavernier.
The Millers players who trooped off the Highbury Stadium surface did so dejectedly, mindful that they might never have a better chance to reach Wembley and lift silverware.
Deep-seated disappointment too for manager Steve Evans, who had a tetchy evening on the touchline and chairman Tony Stewart, whose pre-match hunch that the Rotherham would make it through to the showpiece in the capital on March 30 and face League One rivals Peterborough United sadly proving inaccurate.
Home boss Graham Alexander may have been forced to rue late equalisers to deny his side victories in their previous two home matches, but he was almost left to bemoan an early concession last night.
The hosts were indebted to goalkeeper Davies, who had to make a scampering save to turn away a rasping low strike from Alex Revell, which took a significant deflection before arrowing towards the far corner.
Fielding a 4-3-1-2 formation, the Millers were the early risers, with Blackpool loanee Dicko, cleared to play along with fellow loan players Haris Vuckic and James Tavernier – all refused permission to feature in the FA Cup on Saturday – heading wide following Ben Pringle’s free-kick.
But out of nothing, a desperate moment from ex-Carlisle custodian Collin handed a gift-wrapped opener to the hosts.
Their first bonafide effort on goal was a weak low shot from midfield man Hughes, but his token effort inexplicably crept through the legs of Collin, who made a real hash of it.
It represented an untimely blow for Rotherham, who had hitherto looked the more likely, but they soon dusted themselves down with Kieran Agard, playing on the right, soon seeing his low shot on the turn saved by Davies.
The goal provided the platform for Fleetwood to start playing some measured passing football, but without substantive further chances as the visitors managed to clear their lines.
And it was the Millers who finished the half on top, with captain Craig Morgan planting a header from Ben Pringle just over before Tavernier’s angled drive which deflected just wide.
Evans’s side cranked up the heat on the restart and were desperately unfortunate not to level when a brilliant swivel from Revell ended with his goalbound low shot striking the post, with his fine effort worthy of a goal.
The pressure continued with Agard firing into the side-netting before the Millers finally get their just rewards in the 55th minute.
Revell’s low shot was diverted towards the net by Mark Roberts and despite Davies making a last-ditch block, Dicko was obligingly on hand to tap home from close range in front of the visiting contingent for his third goal in four outings after joining from Fleetwood’s near-neighbours Pool.
It proved the catalyst for an end-to-end remainder of the game, with Steven Schumacher soon firing a fierce free-kick from a tight angle just off target before Collin denied Antoni Sarcevic at his near post.
With the pace of Agard and Dicko causing problems at the other end in a half which saw the Millers play with more urgency, Fleetwood found themselves increasingly stretched.
But a bolt from the blue from McLaughlin, who capitalised on a weak clearance from Ben Pringle, produced the equivalent of a pressure-reliever as the visitors stood off – and the feeling it just might be the hosts’ night.
That was confirmed late on when Davies produced heroics to tip over Frecklington’s 25-yarder before making an instinctive save to deny Tavernier, off target with a stoppage-time free-kick.
Despite laying siege in five minutes of stoppage-time as away players poured forward, the hosts held out with the play-off chasing Millers left to concentrate on the league, as the cliche goes.
Fleetwood Town: Davies; McLaughlin, Roberts, Pond, Taylor; Blair (Brown 78), Schumacher, Hughes, Evans (Cresswell 89); Sarcevic, Tyson (Carr 76). Unused substitutes: Murdoch, Lucas.
Rotherham United: Collin; Bradley (Brindley 46), Morgan, Arnason, Tavernier; Agard, Frecklington, Pringle; Vuckic (Davis 79); Dicko, Revell. Unused substitutes: Shearer, Tubbs, Rowe.
Referee: S Duncan (Northumberland).