Outside-half Matthew Jarvis kicked 12 points with former Wizards man Richard Carter and Kyle Evans scoring second-half tries.
Merthyr were made to sweat at the death as Aberavon pressed for a late winner, but Lee Jarvis’ men did enough to seal title glory.
Their coronation as champions at the highest level of semi-professional rugby in Wales caps a remarkable journey from the lower leagues to lifting the title in their first Premiership season.
Just three seasons ago, Merthyr were playing in Division 1 East.
Aberavon topped the Premiership before the midway split in January, but finished runners-up to Merthyr in Tier 1 during the second part of the league season.
The Ironmen thumped RGC 1404 35-7 in their semi-final, while Aberavon beat Bedwas 31-24 to book their place in the last two.
BAFTA award-winning actor and Port Talbot local Michael Sheen was in the crowd at the home of Aberavon to support his beloved Wizards.
But the Hollywood star saw his side get off to a slow start despite sunny conditions as Merthyr moved into an early lead, Jarvis putting the visitors on the board after two minutes with a simple penalty.
But Aberavon responded brightly and found the game’s first try.
Lock Ben Davies was the man who crossed after powering his way over in the corner. James Garland was wayward with the extras after a crosswind blew his effort well off course.
A scrappy encounter ensued with both teams well aware the title was on the line. Merthyr, though, had the better of the territory and Jarvis restored their lead.
On his 379th and final game for the club, Aberavon skipper Ian Moore gave away a penalty just before half time after a high tackle on wing Carter. Jarvis duly kicked the three points.
Aberavon ended the first half the stronger and looked certain to score another try, but the Merthyr defence held firm as the Ironmen went into the break ahead.
Garland kicked a penalty 10 minutes after the interval to narrow Aberavon’s deficit to one point and Jarvis then uncharacteristically skewed a three-pointer wide as the tension heightened.
Alex Jeffries’ surging run looked set to tee up another home try, but the Wizards just couldn’t quite find the final pass and Merthyr somehow managed to clear their lines.
Garland kept the scoreboard ticking and put the Wizards back ahead on the hour mark and only a last-ditch tackle to halt a charging Jay Baker stopped Jason Hyatt’s men scoring in the corner.
The usually accurate Garland then missed with a penalty attempt, allowing Merthyr to turn the game on its head in the final 15 minutes.
Carter capitalised on Garland’s clearance kick to score behind the posts, before Justin James’ kick was gathered smartly by Evans who scored in the corner to virtually seal victory.
Aberavon pressed for a late turnaround and teed up a dramatic finale when Sam Williams crossed and Garland kicked the conversion with seven minutes left on the clock.
But it was too little, too late as Merthy held firm and a late Jarvis penalty put the gloss on their historic success.
