This was a thrilling contest and Shannon used the advantage of a strong wind in the opening half to build up a 13-point lead at the interval.
Shannon’s out-half Ronan McKenna, who scored all his side’s points in the drawn game last week, was again the architect of his side’s success.
His beautiful chip into the corner on 60 minutes was pounced on by winger Greg O’Shea, who touched down and McKenna’s conversion left Clonmel with an uphill battle after that to retain their title.
The Limerick side, boosted by this score, showed all their experience as they withstood everything Clonmel had to offer in the final quarter.
McKenna kicked Shannon into the lead after four minutes with a long range penalty. Clonmel responded immediately, and from a penalty on the Shannon 22 they opted for touch before finally barging their way over the line for Stephen Pyke to touch down.
Shannon were back in front from the restart with prop Niall Horan touching down and McKenna converted.
Midway through the half McKenna increased his side’s lead with a penalty.
From the kick off Clonmel were awarded a penalty on the Shannon 22, and again they opted for touch and mauled the ball over the line for Ronan Cross to touch down.
David Quinlan scored Shannon’s second try after a drive by the pack and McKenna converted for a 20-10 lead.
Conor Cooney kicked a penalty for Clonmel, but two penalties by McKenna left Shannon in control at half time.
Two penalties by Cooney had the margin down to seven in the opening minutes of the second half.
But, with Clonmel now over-elaborating in the wet conditions, Shannon hit back with O’Shea’s try for a famous victory.
The Munster Junior Interprovincial side finished their campaign with a 40-33 win over Connacht in Creggs to finish runner’s-up to Ulster.
Kieran Downey scored two tries for the winners and Greg Higgins, Warren Kelly and Eoghan O’Dwyer got one each. Higgins kicked a penalty and Eoin Geary added three conversions and two penalties.
Thomond defeated Highfield to lift the Munster Junior 2 Cup at Wilton with a 13-10 victory.
David Guerin and Conor McMahon scored tries for Thomond and Damien Carmelo kicked a penalty.
Highfield replied with tries from Neal Griffin and Alan Spillett.
C Cunnane; R Hunt, W Leonard, T O’Neill, G O’Shea; R McKenna, J Cullen; T Cusack, T Chan, N Horan; E McCabe, J Ryan; B Downey, K Brown, D Quinlan.
L Cronin, G McNamara, C McCallum, S Horgan, R O’Doherty.
C Cooney; G Carroll, L Hogan, B Condon, D Cass; D Cadogan, A Sheehan; B O’Kelly, G Mulcahy, P Keating; M Barry, R Cross; S Pyke, D Foley, N Melbourne.
B Lawlor, J Gallagher, T Cantwell, M Lyons, D Lyons.
R O’Sullivan (MAR).