Samoa, meanwhile, heads to a two-match playoff with the runner-up of European qualifying.
Fiji scored five tries to secure the bonus point win.
With Samoa losing by more than 20 points, island neighbours Tonga now qualify for Japan while Samoa faces the prospect of a repechage match against the victor of Czech Republic or Portugal versus the second-place team in the 2016-17 Rugby Europe Championship.
If Samoa wins its repechage it might have an easier road in World Cup pool play, playing in Pool A with Ireland, Scotland, Japan and a European qualifier.More news: Bakayoko Joins Chelsea From Monaco
Henry Seniloli scored a hat-trick as Fiji won 38-16 to lift the Pacific Nations Cup for the third consecutive year.
Samoa's loss handed Oceania's second berth to Tonga, which is now in the same pool with England, France, Argentina and the United States.
As for Fiji, they finish top of the Oceania group and go into Pool D, along with Australia, Wales and Georgia, with a last spot still to be decided. Seniloli was rewarded in all three tries for his outstanding supporting play, staying on the shoulder of fullback Timoci Naguca to score his first.