Japan scored four tries in the first half and three in the second of the semi-final to give Eddie Jones his third straight win after a tricky start to his second stint as head coach.
Jones will hope to keep the streak going in next weekend's final in Osaka against Fiji, who beat the United States 22-3 in the first semi-final on Saturday.
"It was a good step up for the team," said Jones, whose side beat Canada and the United States to top their group.
"Samoa are obviously a much stronger opposition than USA or Canada. I thought we started the game really well with great intent, particularly playing against a strong wind."
Jones said his team would have to improve their defence around the ruck if they want to lift the trophy for the first time since 2019.
"As much as we're pleased to be in the final, our only aim is to win the final," said the Australian.
"We're going to play against a high-quality team in Fiji and we've got a good week's preparation ahead of us to get ready."
Dylan Riley got Japan off to the perfect start with a try in the sixth minute.
Riley, who scored a superb solo effort against the United States in the group stage, collected a through kick and touched down before Seungsin Lee added the conversion.
A penalty try four minutes later increased Japan's lead and saw Samoa winger Elisapeta Alofipo sent to the sin-bin.
Samoa dug in despite the setbacks and scored a try through Tuna Tuitama in the 13th minute.
But Japan restored their cushion just minutes later when Tomoki Osada crossed the line on the right wing.
Samoa reduced the deficit with two penalties but Japan added a fourth try before half-time when Lee touched down just before the hooter.
Kanji Shimokawa scored another four minutes after the restart, before Melani Matavao pulled one back for Samoa.
Further tries for Japan's Shinobu Fujiwara and Taichi Takahashi and Samoa's Lalomilo Lalomilo rounded off the scoring.
