Visitors Nefyn started brightly dominating the early stages and on 10 minutes Guto Sion Roberts broke the deadlock after a scramble in the goalmouth. Bontnewydd, with a side that featured six 16 year-olds, then weathered the storm with the young defence marshalled by captain Alun Guto Williams.
As the first half progressed Bont gradually gained a foothold in the game and were rewarded for their perseverance when 16 year-old Dion Davies beat three men and unleashed a curling drive to score the equalising goal.
In an evenly matched second half Nefyn winger Jos Lloyd looked the most likely to unlock the home defence.
However, home keeper Sion Davies made a string of fine saves to frustrate the visiting strikers.
With chances at both ends, in the 73rd minute a deep cross from Bontnewydd substitute Dylan Price found player-manager Ian Pleming at the far post and the former Glantraeth hitman calmly finished with his left foot from four yards out.
Nefyn then pushed for an equaliser but the form of Davies and a failure to convert several half chances saw the home side retain their lead.
Livewire Cai Penny Williams extended Bont's lead in the 83rd minute when he latched on to a through ball from Pleming. The pacy front man made it 2 goals in 2 games when he left Nefyn's defenders for dead to beat keeper Alyn Williams.
In an end to end finale Nefyn scored a 91st minute penalty when Josh Dorkins calmly slotted home, only for the referee to blow the whistle for full time and Bontnewydd fielding nine teenagers gained their first victory of the new season.