Osian Pritchard proved to be the match winner on 72 minutes when he punished home keeper Richard Morgan's fluffed punch from a Jon Peris Jones flag kick.
It was a reward for the Bodorgan boys' bombardment of the home goal in the second period as
the hosts lost a bit of composure.
Playing up the slope, Glantraeth were the first to threaten after 25 minutes of sterile stuff, but a Paul Rowlands effort was deflected for a corner.
However, the hosts went close when a Dylan James dipper cleared the bar by inches, but David Alan Jones headed a Peris Jones cross wide from a great position at the other end.
The Glantraeth player was the culprit again early in the second period, heading over another Peris Jones cross.
The visitors were controlling the game but were nearly undone when Llyn Hughes headed wide in a rare Penrhyn sight of goal
Morgan saved well from Peris Jones and Richard Owen's long range effort whistled inches wide, and once again, the hosts had some encouragement when it needed a Llion Davies touch to deflect a Chris Williams shot.
Pritchard's goal brought rewards to the visitors and they should have doubled their tally when Chris Saxon set up Peris Jones, but the normally deadly finisher fired straight at Morgan.
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