Mariner was denied by the bunker just before halftime on Sunday, when it was deemed there was insufficient evidence he had got the ball down on the line.
Initially sent up as no try due to concerns over a double movement, bunker official Chris Butler cleared that part but ruled Mariner did not get to the tryline.
A converted four-pointer would have potentially put Samoa up 18-6 at halftime, but they instead took a 14-6 advantage after a penalty goal.
Mariner would not blame the 36-14 defeat on the decision as the Kiwis ran down the Pacific powerhouse in the second half, but was adamant it was a fair try.
"I knew I scored it, but I just had to get on with it and move on," the Brisbane Broncos winger said.
"I don't know how your arm can be over the try line but the ball doesn't touch the ground. I felt it and I tried to celebrate, but I was still held down.
"It was a 'what if' (moment) but we still had a lead going into halftime.
"So whether I scored or not, we still had a full half to play footy."
New Zealand's Pacific Cup triumph proved they should not be discounted as a challenger to Australia at next year's World Cup.
Samoa are also clearly building after their fairytale run to the 2022 final.Â
After bringing Payne Haas in this year, Stephen Crichton, Spencer Leniu and Hamiso Tabuai-Fidow intend to return next year from injury.
So too could Tino Fa'asuamaleaui, with the Australia and Queensland prop weighing up his options.
Samoa have seemingly gone ahead of Tonga to be the most dangerous Pacific Island team, beating them 34-6 a fortnight ago.
They also should have beaten the Kiwis in the opening game of the Pacific Cup, blowing chances late in the game to claim their first victory over a tier-one nation.
But they piled too much pressure on themselves in Sunday's decider, the team's biggest game since the 2022 World Cup.
"I thought we made some good steps in some important areas," coach Ben Gardiner said.
"Our mental resolve was really good in the first game and the second game ... it could have been a little bit better.
"In big matches it's not just about the footy, it's also about the mental game and making sure you're also mentally in the moment in the right moments.
"That's something we can definitely learn from for next year."
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