Laurie Harries had given Quins a 3-0 lead with a simple penalty, the kick the only score of what was a tight, competitive first half.
Bethan Preece levelled things up for Neath before Harries' superb solo performance continued as she crossed for the first try of the day to put her side back into the lead.
But when Kath Gravell went over for Neath, the game went into extra time. Like the first 80 minutes, added time was tight and fraught with tension but Neath full back Karen Mayze proved the difference as her late, late score, converted by Preece, secured the win.
Neath had been dominant in the early stages, Shona Powell-Hughes at her powerful best from No. 8. But despite Neath being completely dominant at scrum time and seeing plenty of ball, it was Quins who took the lead via a Harries penalty.
On a wet day, there were a number of mistakes from either side but despite a break from Harries and a sin binning for either side, it remained 3-0 at the break.
The second half was barely seconds old when Preece levelled the scores with a penalty for Neath. They weren't level for long though as a superb Harries score made it 8-3 to the Quins. The build-up to the score had seen the Quins playmaker suffer an injury and when she eventually hobbled off 10 minutes later, it dealt her side a huge blow.
Neath made the most of her absence and when Gravell squeezed over in what were increasingly wet conditions, the game was bound for extra time.
The added time was tight and tense but Mayze's score, converted by Preece, saw Neath crowned champions.
The Cup final formed part of a hugely successful day of Women's rugby at Llandovery RFC with seven games taking place in total.
Women's Finals Day results:
Vase Final: Nantyffyllon 30-5 Colwyn Bay
Under 18's Final: East 3-29 West
Bowl Final: Barry 3-20 Gwernhyfed 20
Trophy Final: Maesteg Celtic 34-12 Seaview
Plate Final: Seven Sisters 22-12 Caernarfon
Shield Final: Gorseinon 17-18 Blackwood
Cup Final: Cardiff Quins 8-15 Neath Athletic