The result, which was the second time this season that the side on the bottom had beaten League One's leaders, allowed incoming All Black coach Dave Rennie's Kobe Steelers to return to the top of the standings at Saitama's expense after they beat Mie Heat, 24-19.
Having endured bumpy rides, Cheslin Kolbe's Tokyo Sungoliath and Richie Mo'unga's Brave Lupus Tokyo both finally qualified for the finals with a week to spare.
Sungoliath, regarded as royalty in the Japanese domestic game, ended a club record five-game losing spell when they overpowered Steve Hansen's Verblitz 54-38.
Two-time defending champions Brave Lupus, who earlier in the competition lost seven games running, held off Shizuoka BlueRevs 34-29 to lock up the sixth spot for the play-offs.
Heat, Verblitz and the BlueRevs are all now done for the season.
Third-placed Spears Funabashi Bay kept their hopes of a top two finish alive when they hammered BlackRams Tokyo 52-8.
Just two points separate Kobe, the Wild Knights and the Spears on the standings.
Sagamihara Dynaboars will join D-Rocks in this month's relegation series after their 31-22 defeat by Yokohama Eagles.
In Division Two, Wallaby flyhalf Noah Lolesio scored 26 points, taking his tally for the season to 139 from just nine games, as Shuttles Aichi crushed RedHurricanes Osaka 78-17 to earn a place in the promotion/relegation series.
