Ex-Mons hero Hughes sent Shels in front with a 12th-minute spot kick, contentiously awarded after keeper Gabriel Sava was adjudged to have barged David McGill when leaping to collect Hughes’ deflected shot.
Hughes threatened Sava’s goal again in the 21st minute, ending a fine passing move with a curling shot that just went wide.
Shels’ fluent passing made them a constant threat in the first half but United dug in and went in at half-time heartened by a decent attacking spell during which midfielder Eric Foley came close with a rasping 20-yard effort.
Shelbourne invited Mons on in the second half and almost paid when Paul Whelan headed against the bar.
Fabio O’Brien then had a penalty appeal rejected when he went down under keeper Dean Delany’s challenge.
A stretched United defence were lucky to escape when Shels sub Karl Bermingham drove wide at the end of a 73rd-minute counterattack.
Bermingham then set up Brendan McGill only for the winger to volley over.
Delany denied O’Brien at his near post as the game entered a fraught final 10 minutes and Alan Byrne came close with a header but Shels defence, which has only conceded nine goals this season, held firm.
MONAGHAN UTD: Sava; Whelan, A Collins (D Byrne 86), A Byrne, Grimes; Reilly, Foley, R Brennan, Marks (Isichei 65); O’Brien, S Brennan (Tierney 76).
SHELBOURNE: Delany; Matthews, Ryan, Boyle, Fitzgerald; D McGill, James, Cassidy, B McGill (Clancy 88); Hughes (Bermingham 70), C Byrne.
Ref: John McLoughlin (Athlone).