Jamie Gavin gave Garryowen a 3-0 interval lead with a penalty.
Alan Ross put the home side ahead with a try after five minutes of the second half and it was only in the final ten minutes that Constitution made sure of victory.
Sean Óg Murphy kicked a penalty for an 8-3 lead and three minutes from time he added a try and a conversion before Eoin O'Donnell scored a second try on the stroke of time.
Waterpark who came to Musgrave Park seeking their first Junior Two Cup South title after their big win over defending champions Tralee in the semi final were no match for Old Christians who ran out deserving 37-7 winners to win the trophy for the third time after a forty two year gap.
Despite playing into a strong wind in the opening half the Rathcooney side led 20-0 at the break. Brefni O'Callaghan, Paudie Sheehan, James Caples, Stephen Twohig, Darragh Daly and Gavin Tobin were try scorers for Old Christians; Dave Scannell added a drop goal and Aidan Tobin kicked two conversions. David Latimer replied with a try for Waterpark and Richard Halley converted.
Killarney did a unique double in Kerry defeating Tralee 10-5 to win the Galwey Foley Cup to go along with the McElligott Cup won earlier in the season. Mike Henderson scored a try for the winners and Cian Kingston added a conversion and a penalty.
Shannon-St. Mary's won the All Ireland Under 19 Cup with a 22-10 win over Ulster champions Malone at Naas, but there was no joy for Bruff who lost 21-7 to Navan in the Under 17 decider.
All Ireland Bateman Cup Final: Ballymena 6, Garryowen 24;
Junior Inter Provincial: Connacht 13, Ulster 10;
Leinster 16, Munster 20;
Munster Seconds League Final: Cork Constitution 20, Garryowen 3;
Garryowen Cup Final: Cashel 37, Nenagh Ormond 21;
Junior 2 Cup South Final: Old Christians 37, Waterpark 7;
North Munster Under 21 Cup: Young Munster 16, Garryowen 11;
All Ireland Under 19 Cup Final: Shannon-St. Mary's 22, Malone 10;
All Ireland Under 17 Cup Final: Bruff 7, Navan 21;
South Munster Under 17 Plate Final: Cork Constitution 21, Skibbereen 11;
South Munster Under 15 Plate Final: Highfield 5, Mallow 8;