The visitors got off to the best possible start on 29 minutes through a John Kavanagh own goal.
Shels' doubled their advantage in the 44th minute after David O'Sullivan netted from the penalty spot, but Izzy Akinade fired back for the home side just a minute later to leave it 1-2 at half time.
A superb Gavin Holohan strike on 79 minutes levelled the tie, and despite a dominant Blues' display for the remainder of the game, Shelbourne held out for the draw.
FT: Waterford 2 Shelbourne 2
All eyes will be on the RSC next Friday when Watearford FC host Derry City in what's their first game back in the top flight of Irish football since 2007.