Just after the restart Sadou Diallo’s effort was palmed away by Conor Kearns before Boyd sent a right-footed shot wide.
Maher was nearly penalised for a mistake in the 54th minute after the Derry stopper advanced from his line to try and collect a long ball and missed, but Sam Todd was able to clear Evan Caffrey’s chance from under the crossbar.
Tiernan Lynch’s men went straight down the other end and broke the deadlock with Duffy cutting in from the right wing before sending a strong shot into the top left-hand corner, leaving Kearns with no chance.
Half-time substitute Alistair Coote looked dangerous for Shelbourne, but the Derry defence were able to deal with any threat created.
In the final 10 minutes of the game, the home fans appealed that a cross into the box struck the hand of Todd. However, referee Neil Doyle waved the gesticulations away.
The Candystripes return to action and are in Dublin once again on Monday when they travel to face St Patrick’s Athletic.