It was a deserved victory for Alan Mathews’ side who had tried to win the game from the start.
Hughes had put himself about giving the Derry City defence no shortage of problems, but it was his gamble in the 70th minute which reaped handsome dividends.
Having anticipated a Shane McEleney header back to keeper Ger Doherty, Hughes burst in, intercepted the pass and guided the ball home at the second attempt.
After a poor first-half, Derry’s Stephen McLaughlin was first to threaten when he went close following a Rory Patterson cross. But Shels substitute Anto Murphy’s superb strike from 25 yards forced Doherty into a superb one-handed save.
The home keeper again burst to the fore again in the 58th minute when saving a David Cassidy effort as the visitors continued to push forward.
But it was Hughes who had the final say when taking advantage of that defensive slip-up with 20 minutes remaining.
DERRY CITY: Doherty; Madden, S McEleney, McCallion (McDaid 82), McCaffrey; P McEleney, Higgins, Molloy, McLaughlin; Morrison, Patterson.
SHELBOURNE: Delany; Ryan, Shorthall, Paisley, Clancy; Cassidy, Dawson, Cronin (Murphy 41), Kavanagh (McGill 86); Hughes, Gorman (P Byrne 81).
Referee: D Tomney (Dublin).