The Black & Ambers’ victory sees them move up to third in the table and they remain the only side who are unbeaten during the second half of the season.
Outside-half Matt O’Brien was the hero of the day with a penalty deep into injury time as his team secured a rare win at The Wern.
“It was the third time we had played Merthyr this season and every game has been very tight,” said Newport head coach Craig Warlow.
“We knew we had a decent chance of beating them if we could bring our A game. Before facing us Merthyr had won 16 games on the trot, but I told the boys they had to lose a game sooner or later and why not against us?
“The honest answer is I don’t know if we are good enough to win the Premiership this season, but we are just going to take it one game at a time and keep improving.
“In the first block of the season we mixed and matched a lot and had some mixed results, but now we are a lot more consistent in our selection. A lot of our younger players have been outstanding.
“The likes of Joe Bartlett, Alex Everett and Kyle Taylor have done a really good job while more experienced guys like Matt O’Brien and Tom Pascoe have been very good. I think we have the right mixture of experience and youth in our squad.”
Carmarthen Quins were the biggest beneficiaries from Merthyr’s slip-up.
Their 23-12 victory away at Cross Keys catapulted the West Walians to the top of the table.
A try from Shaun Jones and 18 points from the boot of Steffan Marshall was enough to secure the points.
RGC1404 also benefitted from Merthyr’s surprise defeat with their narrow 16-12 win over Aberavon putting them above the Ironmen in the table.
Elsewhere, Llanelli thrashed Bargoed 48-7 at Parc Y Scarlets, while Pontypridd edged out Bridgend 38-37 in a thrilling game at Sardis Road.
That result puts Pontypridd fifth in the table and level on points with Newport and Cardiff.
Ebbw Vale comfortably overcame Neath 22-6 to go up to seventh, Bedwas edged out Llandovery 13-6, while Cardiff thumped Swansea 53-25 at Cardiff Arms Park.
