Mark Jones’ men had Tiaan Loots and Ross Davies to thank as their tries either side of half time proved enough to take the Cup back north.
Pontypridd scored through Lewis Williams just before the break, but it was not enough to secure a seventh knock-out triumph.
RGC thought they had the game’s first try after three minutes, but Alex Schwarz’s effort was ruled out by the TMO after replays showed the scrum-half spilled the ball on the try-line.
It was a battle of the defences in the opening 20 minutes as both sides had half chances to break the deadlock.
Pontypridd’s Ben Jones saw a penalty fall well short and missed with another attempt minutes later.
But there were no issues for New Zealander Jacob Botica, who drilled his first penalty between the uprights to put RGC ahead.
And the outside-half played a hand in setting up the first try. The son of All Blacks legend Frano reversed the ball inside for the charging Loots to cross at the posts.
Pontypridd got on the board soon after as Wales Under-20 star Jones adjusted his radar to slot a penalty and RGC were suddenly up against it when Rhys Williams saw yellow for a high tackle.
The Black and Whites made the most of the extra man with a clever try.
Afon Bagshaw misjudged a high ball and fumbled into touch with the quick-thinking Lewis Williams finding Wayne Evans at the line-out. He returned the favour for the wing to scamper away to the corner.
Jones missed the conversion to leave the match at 10-8 at the break.
Pontypridd were on the charge and RGC went down to 13 when Phil John – who won the National Cup with Llandovery in 2007 – went to the sin bin for killing the ball.
Jones added the resulting penalty to put the his time into the lead for the first time.
Botica put a penalty attempt narrowly wide, but Davies made up for that with a try after scrambling over, with the TMO confirming the ball had touched the whitewash.
The game was still very much in the balance at 15-11 with RGC looking the more likely to score again going into the final quarter.
RGC put themselves in some good positions, but failed to make the most of them as Pontypridd held firm.
Chris Dicomidis’ men crept forward with five minutes to go, but Keiron Assiratti’s knock-on killed their progress and RGC edged over the line for an historic win.
