The Déise were 11 points down when Sean Hayes buried his second goal of the game on 41 minutes but Tipperary only scored once more.
Things still looked bleak for Waterford heading into added time as they trailed by seven points but there was still one twist left in the game.
Michael Kiely came up from centre-back to fire in their first goal on 60 minutes and forced another home moments later to cut Tipperary’s advantage to just one.
Kiely then added a free to square the game up and Waterford hit the lead when Gavin Fives came down the left wing to score a wonderful individual point that proved to be the winning score.
Tipperary had bossed the first 40 minutes of the game but completely switched off after Hayes’ second goal and were punished as a result.
James Devaney had Tipperary in firm control from placed balls in an opening quarter that saw them lead 0-5 to 0-2.
Things got even better for the Premier County on 16 minutes when Hayes found a way past Dean Beecher from an acute angle with a powerful low shot. That helped Tipp into a 1-6 to 0-3 advantage at the break.
Devaney was at it again early in the second half with his sixth point of the game that was quickly followed up by a Devon Ryan goal.
Kiely kept Waterford in touch with two fine long-range placed balls but the game looked beyond Waterford when Hayes found the net for the second time, taking his tally to six goals from three games.
Kiely continued to keep Waterford’s hopes alive with some superb efforts from long range. The game still looked to be going Tipperary’s way heading into added time as they led by seven points.
Waterford subs David Byrne and Christopher Kavanagh sent over fine points to help the comeback on its way before Kiely’s devastating double and Fives’ solo effort saw them home.
M Kiely (2-5, 2 frees, 2 65s); S Keating, C MacCraith (1 s/l) (0-2 each), P Leevy (1f), D Byrne, C Kavanagh, G Fives (0-1 each).
J Devaney (0-7, 6 frees); S Hayes (2-0); D Ryan (1-0), K O’Kelly (0-2).
D Beecher; G Fives, R Furlong, J O Floinn; S Fitzgerald, C Wadding, M Kiely; R Tierney, K Mahony; C Keating, O O Ceallaigh, T Loftus; C MacCraith, P Leevy, J Power.
S Henley for Fitzgerald (h-t), A Organ for Loftus (38), C Kavanagh for Leevy (45), G Corbett for Mahony (48), D Byrne for Keating (48).
A Browne; C O’Dwyer, C Whelan, K Hayes; J Ryan, F Purcell, S Phelan; M Hackett, J Campion, D Ryan, J Morrissey, K O’Kelly; K Maher, S Hayes, J Devaney.
C O’Farrell for Morrissey (h-t), M O’Shea for Maher (45), B O’Connor for Phelan (55), O Larkin for Hackett (55), R Renehan for Hayes (58).
R McGann (Clare).