Japan finished at the top and USA at the bottom of Pool B in the six-team PNC tournament. Fiji beat Samoa 29-15 earlier on Saturday (local time) to finish atop Pool A.
Fiji will play Canada and Japan face Tonga in semi-finals next weekend in Denver, Colorado, while the USA play Samoa for fifth and sixth places.
The top five teams qualify for the 2027 World Cup in Australia.
Japan and Fiji had qualified before the Pacific Nations Cup. The other semi-finalists and the winners of the playoff for fifth also will qualify, while the sixth-placed team will go into a regional playoff against a South American team.
Ranked 18th in the world, the USA faced almost a mission impossible on Saturday to beat Japan with a bonus point and by a wide margin to displace Canada from the semis. Canada beat the Americans in the first round of the tournament.
The USA put up a good fight despite conceding four first-half tries, scoring two tries of their own before halftime, both through powerful hooker Kapeli Pifeleti. Japan led 28-14 at halftime.
After conceding three more tries in the second half, the USA showed pluck to score the last try of the match through replacement Payton Telea.
"This is just another step forward for us. Obviously not the result we wanted, but it's a step ahead of the performance we had against Canada," USA captain Jason Damm said.
"The most important step is the next one, so we just have to keep going forward, leave the past in the past, take the learnings from it, apply them and keep pouring energy into what we do."
The strength of Japan's set pieces was a key factor. They packed a powerful scrum in which tighthead Shuhei Takeuchi was a dominant figure, and used a number of lineout variations.
Back-rowers Ben Gunter and Amato Fakatava scored on the short side of surging scrums, and captain Werner Dearns rounded a lineout to score in the first half.
Kanji Shimokawa ensured all three starting back-rowers touched down when he scored at the end of a backline counter-attack.
Fakatava and Dearns completed doubles in the second half.
Winger Kippei Ishida got one for the backline, scoring Japan's seventh try with 10 minutes remaining.
Seungsin Lee kicked six of seven conversions.
