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.
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.
