The Irish winger with a Welsh name met his striking match in Karl Connolly, whom Wrexham recruited from Napoli - a Merseyside park outfit - but, despite a second-half siege, Brian Flynn's battlers could not prevent Wimbledon claiming a trip to Huddersfield.
Wrexham struck first with a seventh-minute goal fashioned by one of four survivors from the team who famously knocked out Arsenal six years ago, and finished by another. Gareth Owen ran at the heart of Wimbledon's defence, shaking off Kenny Cunningham before passing low across the six-yard area. Neil Roberts lunged at the ball, only for it to stick beneath his foot. As he careered on, the ball stayed behind, almost motionless. Connolly pounced to stab it beyond Neil Sullivan.
The Premiership side's response was initially imbecilic - Vinnie Jones twice raised his arms to opponents and was cautioned - and then irresistible. Hughes equalised in the 18th minute with a thunderous volley from 20 yards which shook the inside of the left-hand post before nestling in the net.
Eight minutes later, Hughes fired Wimbledon in front with a powerful curling shot from inside the penalty box after the ball broke to him from Brian Carey's challenge on Marcus Gayle.
There was considerable irony to the Dons' third goal, nine minutes before half-time. As Neil Ardley's corner swung in, Gayle rose at the near post to glance his header past Andy Marriott, exactly as he had done in the last act of the first meeting.
Mr Dunn, whose appointment to the replay Wimbledon had considered challenging after his pedantic time-keeping at Selhurst Park, again appeared ready to deny Gayle his glory. But after consulting a linesman, who apparently believed it had been a free-kick, he awarded the goal and left the pitch to a chorus of jeers from Wrexham's fans.
The tie required the Second Division hosts to score next, and they obliged 90 seconds after the interval. Roberts' cross reared up off a defender's head, giving the unmarked Connolly a free header for his 12th goal of the season.
Mr Dunn's popularity in North Wales plummeted further when he promptly refused Wrexham's penalty appeals as Mark McGregor fell under pressure from Alan Kimble. Wimbledon, however, lived dangerously in the final minutes, the ball flashing across Sullivan's goalmouth with no red shirt able to apply the touch that would have earned extra time.
Wrexham (4-4-2): Marriott; McGregor, Ridler, Carey, Hardy; Phillips, Ward (Chalk, 84), Owen, Wainwright; Connolly, Roberts. Substitutes not used: Brace, Brammer, Spink, Cartwright (gk).
Wimbledon (4-4-2): Sullivan; Cunningham, Perry, Blackwell, Kimble; Ardley, James, Earle, M Hughes; Cort (Ekoku, 76), Gayle. Substitutes not used: C Hughes, Solbakken, Clarke, Heald (gk).
Referee: S Dunn (Bristol).Reuse content