Samu Kubunavanua came off the bench despite his sore ankle to dive over twice late in the piece, while big Timoci Seruwalu scored in each half as part of an excellent match on attack and defence.
Marton hooker Paul Scott-Chase typified the never-give-up attitude of his team.
Ngamatapouri coach Richard Carston acknowledged Marton's effort.
"They were the only side that looked anything like it in the first round. We knew they would come up here to play.
"[We] lost our way a little bit there, but I asked them at halftime to settle down and stick to the gameplan.
"We are still just a second-year team."
Marton coach Dennis Peeti-Tucker acknowledged both the belief of players and the large contingent of supporters that they could have pulled the upset against their highly vaunted opposition.
"These boys play with heart, that's what it's all about. Good turnout, Marton supported us."
The club will now petition the WRFU to also join Ngamatapouri in heading up a grade, returning Marton back to the top after they folded into one Senior team in 2015.
"We want to go up as well because I think we can beat them in the Prem's," said Peeti-Tucker.
"Heaps of people from Marton want to come back and play."
It was looking all one-way traffic early as Baleitavuku dove under the posts as Ngamatapouri attacked straight from the kickoff and their dominant loose forward trio of captain Reid Belton, and representative players Malakai Volou and Bryn Hudson took the hitups and made short passes.
Fullback Chris Belton chipped ahead and got the bounce before being turned over right on the tryline by Marton flanker Glenn Weitenberg, another standout, but the ball quickly went wide for prop Wade Nicol to score.
Ngamatapouri's forwards came through to pressure Marton halfback Bryant Galpin, who bravely stood his ground, but the favourites had the momentum as Hudson tried a switch play at the back of the ruck for hooker Jack Hunter to smash his way over.
But Marton got back a little territory as Ngamatapouri would make mistakes or catch the ire of referee Glenn Collins - Raukawa kicking the first of three penalties - then a good sideline run by John Kiilisi brought them back down to the line and after another penalty, they tapped it and former representative midfielder Soonalote Tauailoto bumped off one tackler to dive over.
Ngamatapouri hit back as Hudson went on the burst and the ball eventually went up to Seruwalu to show his strength as he hit the contact and pumped through to score.
Yet Marton kept contesting everything, making Ngamatapouri work around the ruck, as a couple of fumbles and free kicks got them in range for Raukawa to add two more penalties and leave his team in striking distance at halftime.
More Marton penalties at the breakdown, where big Ngamatapouri lock Clint Newland was trying to unsettle them, set up a lineout drive from 7m out on No8 Hamish Greer, as Galpin and winger Peter Duxfield each a took drive forward before Scott-Chase pushed his way over to through to close the scoreline to a point.
Minutes later, Marton calmly worked forward from phase after phase and then prop Matthew Haskell fed Duxfield, who dove league-style to plant the ball with his body in mid-air at the corner flag, sending their supporters into raptures.
Ngamatapouri were further stung, as were the Steelform Wanganui selectors, when Hudson went down with another big knee injury, while Volou tried to turn momentum back their way with a couple of surges.
Getting to the line near the right hand touch, Ngamatapouri caught Marton short when they swung back to the left and Seruwalu was unmarked to jog over.
A midfield turnover saw Seruwalu feed centre Michael Nabuliwaqa, who survived a diving tackle and found Kubunavanua, who kept his footing through the last defender's diving tackle to score.
Moments later, Marton again lost control and Nabuliwaqa quickly linked with Kubunavanua, who ran hard at the line and smashed through the last tacklers to take his side out of the underdogs grasp with 13 minutes left.
Both tired sides coughed up the ball or gave away penalties while the clock ticked down to the end of Ngamatapouri's dominant unbeaten season.
Settlers Honey Ngamatapouri 37 (Samu Kubunavanua 2, Timoci Seruwalu 2, Isireli Baleitavuku, Wade Nicol, Jack Hunter tries; Baleitavuku con) bt Speirs Food Marton 26 (Soonalote Tauailoto, Paul Scott-Chase, Peter Duxfield tries; Joey Raukawa 3 pen, con). HT: 22-16.