Fijiana lost the championship for the first time since 2019.
Cassie Siataga was Samoa's star, kicking the winning penalty on full-time and scoring all of her side's 19 points.
That win also gave Samoa the right to play in the Women's World XV Tier 2 competition later this year while Fiji will compete in WXV 3.
"Honestly, I'm really speechless," Manusina captain Sui Pauaraisa said at the post-match media conference.
"We knew that we were the underdogs, we knew we had nothing to lose.