Second-half tries from Dan Hodge, Gerwyn Price and Nathan Trowbridge saw Keys turn around a 13-6 deficit at the interval and secure their first trophy in their 127 year history.
Hodge got his side back into things moments after the restart before front-row forward Price showed the pace of a three-quarter to score from all of 30 metres with Trowbridge's score adding gloss to the scoreline.
Keys' coach Greg Woods praised his side and singled out Price's try as a special moment. "It was an unbelievable try from a hooker in the 60th minute," he said.
"He has been the stand out hooker in the league this year. Cup finals are won on big moments like that."
Woods also paid tribute to the crowd, many of whom had travelled down for the day.
"Obviously the burglars had a fantastic time because there was no one left in the village," he added. "The boys like a party and that's great because I think that shows the team spirit we have here."
In a scrappy but ferocious first 10 minutes both sides struggled to create any clear line breaks. The contact area was fiercely contested though and with both sets of forwards refusing to give an inch, the score remained level.
Finally some running rugby broke out as Pontypridd lock Cory Hill made a superb half break but found little in support. From a similar break moments later, the ball found its way to Matthew Nuthall but the winger knocked on under pressure.
Despite failing to break down Cross Keys' defence, Ponty were soon rewarded with a penalty from outside-half Lewis Williams after their opponents were penalised at a scrum. Williams struck both posts with another penalty but Ponty were not to be denied as they extended their lead with a try after 20 minutes. A fine backs move saw Nuthall squeeze over on the left hand touchline with Williams adding the extra two points.
After slipping 10-0 behind, Cross Keys were further hampered when Rhys Dyer limped off injured shortly after, the scrum-half replaced by Owen Jones. It didn't seem to matter though as Keys got on the scoreboard through a Dean Gunter penalty in the 24th minute. The two sides exchanged a further penalty apiece as Ponty went into the interval ahead 13-6.
Replacement scrum-half Jones enjoyed a brilliant start to the second period as Cross Keys dominated territory. One reverse pass created an opening in the opposition defence before a quickly taken penalty saw his forwards go over.
Referee Sean Brickell sent the decision upstairs and after an age, the try was eventually awarded with the score credited to Dan Hodge. Gunter added the conversion to level things up at 13-13.
After dominating most of the first period, Ponty were suddenly struggling. A clean line break saw Dafydd Lockyer in acres of space but with two men outside him and the try line gaping, the centre inexplicably failed to deliver what would have been a simple try scoring pass. And things got worse. When Ponty were penalised for a high tackle, Gunter kicked his third penalty to put Keys in front for the first time.
Williams soon levelled things up though before he put his team ahead by three with another simple penalty but Gunter quickly hit back for Keys. And straight from the restart Keys' hooker Price found himself in space on the right hand touch line. Showing a brilliant turn of foot, Price outpaced the covering defence and though it looked as if he had a foot in touch, the try was given by TMO Paul Adams. Gunter again struck the post with his conversion as the lead remained at five points.
The tenacity of the game began to tell as the game moved to uncontested scrums but it was Cross Keys who looked the stronger. A break from Mark Popham saw the replacement forward pop the ball up to wing Nathan Trowbridge who went over in the corner leaving Ponty coach Dale McIntosh downbeat.
"If we weren't grieving we wouldn't be human, we owe it to the supporters first and foremost, we've let them down," he said.
"You don't win cups by playing well, you win them by playing very well but I can't take it away from Cross Keys.
"It's great that they have got something out of their season. We lacked composure and did things out of character for us."
Gunter missed the conversion but added another penalty just minutes later as Cross Keys ran away with things to make amends for their British and Irish Cup final defeat to Munster A last weekend.
Man of the match: Rob Nash (Cross Keys)