With the combined results of the 2016 and 2017 cups doubling as World Cup qualifiers, Samoa needed to at least draw with the unbeaten Fijians to overhaul Tonga and reach the tournament in Japan in two years time.
Even a bonus point in defeat might have been enough.
They led 16-14 at half time in Apia but had no answers as Fiji over-ran them in the second half.
Fiji, who secured qualification last week when they defeated Tonga 14-10, scored five tries in total, including a hat-trick to scrumhalf Henry Seniloli.
The result puts Tonga in Pool C, the so-called "Pool of Death", at the 2019 World Cup, alongside England, France, Argentina and USA.
Samoa can still reach the World Cup through the repechage qualification series.
Fiji flyhalf Ben Volavola was immaculate with the boot, kicking five conversions and a penalty for a personal haul of 13 points in the victory.
The win also sealed the 2017 Pacific Nations Cup for Fiji.
“It was a great win and I think our bench was great and it showed in the second half. We were too narrow in the first half and we gave away penalties that kept Samoa in the game,” said Fiji coach John McKee.
“We are proud to have defended our PNC title. It is also our fourth Test win in a row and I am told that is a record for Fiji.
“Of course we have also qualified for RWC 2019 and we will focus on that now. This is a talented group and we have some younger talent emerging also.
"I believe this squad can improve further and our aim will be to make the quarter-finals in 2019.
“It is an ambitious goal as RWC is incredibly hard but you have to be ambitious to succeed.”