Local lad Ethan Boyle struck an injury-time winner to secure an opening night victory for Shamrock Rovers in front of 4,152 fans at the RSC.
Following a lacklustre first half in which the Blues took the lead against the run of play through Kevin Lynch's sumptuous free-kick, Rovers dominated the second half. Aaron Greene's equaliser seven minutes after the restart was coming and Boyle completed the comeback by volleying through a thicket of bodies in stoppage-time.
The meeting of last year's third- and fourth-placed teams featured a number of new faces, primarily for Waterford.
Alan Reynolds included five of his recruits, including former Ireland defender Damien Delaney at the back and Aaron Drinan, returning to the Blues on loan from Ipswich Town.
It was another arrival who made the first major impact on 22 minutes.
Lynch played alongside Robbie Brady at St Kevin's Boys and the former team-mates share their penchant from deadball skills. When Shane Duggan was tripped 25 yards out, the left-back stepped up to curl an exquisite free-kick over the wall and inside the near post of Alan Mannus.
The Rovers goalkeeper has been unworked up to that point, his opposite number Matt Connor the one having to deal with a series of threats. Dylan Watts was first to test the local stopper after just two minutes as his side-footed effort from 12 yards was batted away.
The big home crowd was almost silenced three minutes later. Jack Byrne's wind-assisted free deceived the Blues backline, yet the unmarked Lee Grace failed to profit by glancing his close-range header wide. Goalscorer Lynch then came to his side's rescue by blocking Carr on the line on the stroke of half-time.
It didn't take long after the break for Rovers to level. Carr was unable to get a clean connection on his shot from Byrne's centre but recovered to square for Greene to tap home.
Chances were traded, with Akinade's volley kept out by Mannus but Aaron McEneff's shot which Connor saved illustrated how the contest was swaying in Rovers' favour.
Late pressure finally told when a corner from the right was turned in by right full-back Boyle, much to the joy of suspended manager Stephen Bradley sitting in the stand.
WATERFORD - M Connor; R Feely, K Browne, D Delaney, K Lynch; Z Elbouzedi, B Héry, S Duggan, J Martin (M Kougan 77); Akinade, A Drinan.
SHAMROCK ROVERS - A Mannus; E Boyle, R Lopes, L Grace, S Kavanagh (T Clarke 75); A McEneff, D Watts (G Bolger 68); J Byrne, R Finn, D Carr; A Greene (O Vojic 75).
Ref - G Kelly (Cork)