They had trailed 22-13 but rallied with a superb second half performance to secure the Cup Double, adding to their Bank of Ireland Towns Cup victory last month.
The entire final was played at a frenetic pace, with both sides putting together some fantastic phases, and either of them would have been worthy winners on the day.
It was Ballyclare who notched the first points with a James Creighton penalty, but Skins fly-half Eddie Keys pulled off an outrageous dummy to create the opening for the first try of the game, as he darted under the posts before converting his own score.
Enniskillen were then held up over the line, and the resulting goal-line drop-out fell straight into the arms of Keys. Despite being 40m from goal, he lined up and the executed a perfect drop-goal to make it 10-3.
Another Creighton penalty kept the Hares within touching distance, but the Enniskillen pack worked hard and Neil Rutledge barged over for another try, with Keys adding the extras.
Ballyclare then scored their first try when Peter Gillespie finished off a flowing backline move, with Creighton's kick closing the gap to 17-13.
However, Enniskillen had the final say of the half when Henry Keys touched down from a lineout maul to make it 22-13 at the break.
Clare absolutely flew out of the blocks in the second half, and soon stunned Enniskillen with a quickfire double.
The first saw fly-half Alex Darragh rip the ball in the tackle, and from the halfway line he pinned the ears back and showed searing pace to tear away into the corner and score, with Creighton nailing the tough kick.
The same thing happened almost immediately from the restart, when the Ballyclare defence stole the ball in the tackle, and this time they released captain Joel McBride down the left channel. He sped away from the defence and crashed through a last-ditch tackle to score in the opposite corner and turn the game on its head.
McBride then stepped inside his defender on the next venture into the 22, and dived in to further extend their lead, with Creighton converting to make it 19 points without reply.
Enniskillen burst back into life after kicking a penalty deep into Ballyclare territory, which resulted in the ball going through the backs before James Ferguson touched down, with Keys converting to make it 29-32.
With the game finely poised, Clare wisely took 3 points from the boot of Creighton on their next press into the Skins 22.
As the clocked ticked towards the end, Alex Darragh's sublime crossfield kick was gathered by sub Matthew Fitzgerald, and when Creighton converted to make it 29-42 Ballyclare looked like they'd done enough to win it.
However, Enniskillen continued to work hard and set up a tense finish when Sam Balfour darted in under the sticks, leaving Keys an easy kick to make it a one-score game.
Ballyclare held firm, and the pack which had done exceptional work throughout the game managed to win a decisive scrum penalty which proved to be the last act of a memorable final.
### Team Lineups
Enniskillen
15-9: George Foster; Sam Balfour; James Balfour; Daire Hill; James Ferguson; Eddie Keys; Matthew Dane
1-8: Gavin Warrington; Niall Keenan; Matthew Graham; Neil Rutledge; James Carleton (C); Jack Rutledge; Henry Keys; Michael Rooney
Replacements: Matthew Beatty; Gary Thornton; Oisin Timoney; Paul McConkey; Harry Ingram
### Ballyclare
15-9: Josh Cowan; Owen Kirk; Joel McBride(C); Matthew McDowell; Peter Gillespie; Alex Darragh; James Creighton
1-8: Adam Barron; Matthew Coulter; Ricky Lutton; Luke McIlwrath; Grant Bartley; Aaron Playfair; Jack Milton; Jack Gamble
Replacements: J Black; J Taylor; J Orr, R McIlwaine; M Fitzgerald
