Midfielder Kieran Power received a red card from referee John O’Brien before the ball was thrown in, after an incident which left Martin O’Leary on the ground.
But the numerical deficit didn’t stop the west Waterford side.
Ten points from wing-forward Cathal Curran — all from placed balls — laid the foundation for the victory while Michael Hurney turned in an impressive performance at centre-forward, bagging 1-1 from play.
St Flannan’s were off tempo in the opening half and conceded too many frees which Curran converted time and again.
Hurney’s 21st minute goal came after he scrambled the sliothar into the net, and edged the Waterford three clear (1-7 to 0-7) at the break.
The Ennis outfit stormed back into contention on the restart as a goal from a long-range Stephen Ward effort levelled the tie and made for a tense second period.
The Clare team’s only time in front came when the influential Tony Kelly converted a free to put them 1-9 to 1-9 to the good but their opponents responded in kind with more points from Curran and an excellent effort from play by Michael Hurney.
They led by two heading towards the end before a fine score from Tony Kelly gave Flannan’s hope of a dramatic rescue, but the equaliser they needed never came.
Scorers for Coláiste na nDéise: C Curran 0-10 (9f, 1 65), M Hurney 1-1, M Kiely 0-1, P Curran 0-1.
Scorers for St Flannan’s: T. Kelly 0-5 (0-4f), P Duggan 0-3 (2f, 1 sideline), S Ward 1-0, M O’Leary 0-1, C Cleary 0-1 (f), S O’Donnell 0-1, D Reidy 0-1.
COLÁISTE NA NDÉISE: E Kearns, S O’Donovan, T Tobin, T Burke, E Collins, T Devine, K Sheehan, K Power, C Dunford, C Curran, M Hurney, R Donnelly, M Kiely, K Daly, P Curran.
Sub: B Looby for C Dunford.
ST FLANNAN’S COLLEGE: E Quilligan, D Conroy, J Brown, S Kelleher, G Ryan, T Kelly, A McGuane, C Cleary, M O’Leary, P Duggan, M McGuane, S Ward, B Duggan, S O’Donnell, D Reidy.
Referee: J O’Brien (Cork).