Neath coach Lyn Jones admitted he sacrificed Welsh Premmiership points for Celtic League semi-final security after his side slippped to a second defeat in the space of three days.
Hot on the heels of their 23-14 reverse at Swansea, Jones' makeshift side let in four first-half tries as Ponty ran into a 26-13 interval lead.
International wing Gareth Wyatt led the way with the opening two tries and then Gareth Baber made the home side pay for an ambarrassing slip in defence with a third score.
Brett Davey rounded off the first half with a fourth score to give the visitors' a handy lead.
Newath started the game without James Storey, Dave Tiueti, Lee Jarvis, Andy Moore, Barry Williams, Brett Sinkinson and Gareth Llewellyn. They were all rested ahead of Saturday's Celtic League semmi-final showdown with Cardiff at The Gnoll.
At stake for the winner is a trip to the Millennium Stadium to play either Munster or Ulster in the final on 1 February.
"The Cardiff game is obviously very much in our minds. This game was always going to be a difficult one for us because of that, but we had to rest some of our leading players," said Jones.
"If we could beat Cardiff and reach the final of the Celtic League it would really set up our season."
Kevin James galloped in for a first-half try for the home side and Shaun Connor added a conversion and two penalties.
But a Davey drop goal extended the Ponty lead in the second half and their pack did the rest in tricky conditions.
Alfie Mocelutu grabbed a consolation try for Neath seven minutes from time, which Connor converted, but Ponty hung on for the points.
While the Ponty pack made the real difference, the fact the visitors scored 12 points in the 10 minutes that Neath lock Andy Newman was in the sin-bin, compered to only three by the home side in the 20 minutes Ponty were down to 14 men with Gareth Baber and Richard Parks in the sin-bin, also counted.
Scorers: Neath: Tries: K James, A Mocelutu; Cons: S Connor 2; Pen: S Connor 2. Pontypridd: Tries: G Wyatt 2, G Baber, B Davey; Cons: N Jenkins 2; DG: B Davey.