Goals in injury-time at the end of each half gave Waterford a first league win in Cork since 2011 and first top-flight victory at Turner's Cross since 2004.
Bastien Héry struck in the 48th minute of the first half for Alan Reynolds' side and then, having soaked up Cork City pressure, they counter-attacked at the death, with Zak Elbouzedi on target.
They were unlucky not to have had the lead as early as the tenth minute. Some lovely skill from Héry took him past Alan Bennett and into the Cork area and, while he could have shot, he squared it for Scott Twine, who looked to have tapped in but Mark McNulty made a super save, diving backwards to stop the ball on the line.
At the other end, City struggled to create clear-cut chances, with a nice Graham Cummins drag-back setting up Liam Nash but Kenny Browne did well to block. In the 40th minute, the Rebel Army finally worked Matt Connor for the first time, as Kevin O'Connor's volley from Dáire O'Connor's cross was saved by the goalkeeper's legs.
Coming up to half-time, Twine wasn't far wide from distance but Waterford didn't have long to wait as Héry struck in the third minute of injury-time, creating a chance with nice footwork and sending a low shot to the net.
With the lead, Waterford were happy to sit back and counter-attack in the second half and City struggled to break them down, even after changing to a 4-4-2.
Twine nearly made it 2-0 but shot wide while Sheppard went closest to a home equaliser on 71, Kevin Feely stopping his shot on the line. Cork continued to press and at the death Waterford broke well, with Zak Elbouzedi firing home.
CORK CITY - McNulty; McCarthy, Bennett (Casey 55), McLoughlin, Hurley (Comerford h-t); Buckley, K O'Connor; D O'Connor, Tilley, Sheppard; Cummins (Nash 68).
WATERFORD - Connor; Feely, Browne, Delaney, Lynch (Kougoun 86); Lunney (Chvedukas 75), Duggan; Elbouzedi, Héry, Twine; Akinade (Drinan 65).
Ref - D Tomney (Dublin)