Gavin Corbett struck 1-2 in extra-time to move De La Salle 2-16 to 1-16 in front and on the brink of glory.
With one minute remaining, substitute Jack Lee seized on Flood’s 65 and blasted his shot through a cluster of defenders to level the match.
The Roscrea teenager was only introduced five minutes earlier.
In the next play, Flood belted over the winner and his 12th point in total to leave the Waterford school completely stunned.
The teams were on equal terms eight times overall. On 16 minutes, Mikey Cummins latched onto Darren Kenneally’s delivery and smacked a shot to the roof of the net.
An industrious De La Salle, driven on by captain Cian Wadding at number six, deservedly led 1-4 to 0-2 at that stage. Wind-assisted Thurles replied with six points in a row during a dominant second quarter. Flood scored five (four frees) before Jack Morrissey slipped them ahead for the first time. Paddy Leavey’s free tied it at the break (0-8 to 1-5).
Thurles had a goal disallowed on the restart for a square ball as Devon Ryan arrived too early to bat the sliotar in. Ryan made amends however with 40 minutes elapsed.
Cormac Walsh saved Flood’s initial shot but the vigilant Ryan whipped the rebound to the top corner.
De La Salle posted seven second-half wides, including four placed balls, yet Leavey recovered his composure to knock over two injury-time frees and force an extra 20 minutes (1-11 apiece).
Flood, Ryan, and Jack Morrissey manufactured a 1-16 to 1-12 advantage for Thurles during the first period.
This final took another twist in stoppage time when Gavin Corbett’s effort deceived Conor Stapleton and crept into the cobwebs. Salle kicked on at the start of the second half but Lee’s goal floored them.
D Flood (0-12, 9 frees); D Ryan (1-1); J Lee (1-0); J Morrissey (0-3); J Lanigan (0-1)
P Leavey (0-7 frees); G Corbett, M Cummins (1-2 each); D Byrne (0-2 frees); T Ryan, D Kenneally, K Mahony (0-1 each)
C Stapleton (Dúrlas Óg); K Costello (Dúrlas Óg), P Melbourne (Moycarkey-Borris), F Hanafin (Holycross-Ballycahill); K Hayes (Moycarkey-Borris), J Hickey (Emeralds), J Synott (Roscrea); J Morrissey (Moycarkey-Borris), C Munroe (Thurles Gaels); K Ryan (Upperchurch-Drombane), D Flood (Moycarkey-Borris), M Hackett (Moycarkey-Borris); K Larkin (Moyne-Templetuohy), J Lanigan (Dúrlas Óg), D Ryan (Kickhams).
P Stakelum (Dúrlas Óg) for Munroe (24); J Ryan (Roscrea) for Synott (53); E Purcell (Dúrlas Óg) for K Ryan (54); C Stakelum (Dúrlas Óg) for Larkin (74); J Lee (Roscrea) for D Ryan (74).
C Walsh (Passage); T Dalton (Ballygunner), C O’Neill (Passage), E Reilly (Passage); T Gallagher (Ballygunner), C Wadding (Roanmore), S Harney (Ballygunner); K Mahony (Ballygunner), D Byrne (Erins Own); P Flynn (Passage), P Leavey (Ballygunner), D Kenneally (De La Salle); G Corbett (Ballygunner), T Ryan (Roanmore), M Cummins (Passage).
C Berry (Ballygunner) for Flynn (60); P Flynn (Passage) for Byrne (67); D Byrne (Erins Own) for Ryan (71).
R Moloney (Limerick)