The full-time score in this afternoon's replay was Clonmel 19 points to Shannon's 33.
At half-time Clonmel were by 26 points to 13 and despite having a strong breeze in the second half, the Tipp club were limited to just two Conor Cooney penalties.
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The Limerick side have won the Junior Cup for the first time since 1996.
The Tipp club will have the solace of a Munster Junior League Division 1 title and a Challenge Cup this season.
Ronan Quirke and Niamh Briggs were at today's final for Tipp FM Sport.