City are now rooted to the bottom of the SSE Airtricity League with two defeats in their two opening games.
It was a bittersweet night for captain Oscar Brennan, who scored what turned out to be the winner, before getting sent-off on 80 minutes.
City went close on 17 minutes but Ciaron Harkin’s stinging long range drive was straight at Brian Murphy and the Waterford keeper easily held the effort.
The home side were inches away from taking the lead on 28 minutes but Danny Lupano was unable to get his head onto Will Patching’s superbly delivered left wing free-kick, when he came in at the back post.
Minutes later the visitors broke the deadlock in sublime fashion as Shane Griffin’s 20 yard free-kick dipped up and over the wall and gave Nathan Gartside no chance, finding the keeper’s left hand corner.
Derry equalised with what was the final touch of the half as another super Patching free-kick from the left was nodded on by Eoin Toal and Cameron McJannet was on hand to fire home his first goal for the club.
Waterford regained the lead on 51 minutes as Oscar Brennan fired home the rebound, after his initial penalty was kept out by a diving Gartside, who had incidentally brought down James Waite inside the box.
Joe Thomson was inches away from levelling things soon after but the midfielder’s well hit strike on the half-volley was superbly tipped over by a full stretched Brian Murphy.
Derry should have equalised for a second time on 65 minutes as Jack Malone’s cut-back found an unmarked Patching, but the Dundalk loanee blasted over from close range, with the goal at his mercy.
Waterford were rightfully reduced to ten men on 81 minutes as skipper Brennan received a second yellow card in the space of a few minutes after his tough challenge on Patching.
The ten men nearly conceded another equaliser soon after but Lupano’s close range header rattled the crossbar, in what was Derry’s final chance of the game.
Next up for Derry is an away trip to St Pat’s Athletic this Friday, April 9.
Derry City: Nathan Gartside, Jack Malone, Danny Lupano, Eoin Toal, Cameron McJannet, Danny Lafferty; Ciaron Harkin, Joe Thompson (Caolan McLaughlin 82), Will Patching; Will Fitzgerald (James Akintunde 59), David Parkhouse.
Waterford: Brian Murphy, Darragh Power, Cameron Evans, Oscar Brennan, Kyle Ferguson, Shane Griffin (Oluwatunmise Sobowale 84); Adam O’Reilly, Cian Kavanagh (Daryl Murphy 56), James Waite, Jamie Mascoll, Prince Mutswunguma (Eric Molloy 60).
Referee: Rob Harvey (Dublin).
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