Kobe, who had been kept in the Sunday's game by 19 points off the boot of ex-Chiefs flyhalf Bryn Gatland, were overpowered in the final 20 minutes as the outgoing champions finished with a decisive five-try-to-two victory.
The result locked in the semi-finalists two weeks before the end of the regular season, after Yokohama Eagles beat Sagamihara Dynaboars 43-19 on Saturday, a result which eliminated Verblitz, Shizuoka Blue Revs and Kubota themselves.
Wallaby winger Marika Koroibete was a double try-scorer for the third week running on Saturday as Saitama Wild Knights confirmed top spot in the regular season.
The Robbie Deans-coached side overwhelmed the Steve Hansen-trained Verblitz 40-7, continuing the ex-Wallaby coaches' dominance over the former All Black mentor.
Hansen has not beaten Deans in seven attempts since joining Verblitz after the 2019 Rugby World Cup, with an average losing margin of 20 points in those games.
Despite fielding the star international quartet of the All Black halves Beauden Barrett and Aaron Smith, Springbok backrower Pieter Steph du Toit, as well as Brave Blossoms backrower and captain Kazuki Himeno, they were outclassed by the Wild Knights, for whom Koroibete and Springbok second rower Lood de Jager starred.
Both men scored two first half tries as the Wild Knights motored to a 26-7 halftime lead, with the defeat even more galling for the home side due to managing just one try and being held scoreless for the final 50 minutes.
Tokyo Sungoliath needed a penalty goal four minutes from time by flyhalf Mikiya Takamoto to salvage a 31-31 draw with Shizuoka Blue Revs on Friday night, but it proved enough to confirm a semi-final place after Kobe's subsequent defeat.
An understrength Brave Lupus Tokyo narrowly beat Mie Honda 8-7 on Sunday, while Quade Cooper's Hanazono Liners recorded their first win of the season in upsetting Black Rams Tokyo 34-23 in Division One's other matches.
Former Wallaby second-rower Rory Arnold gained reward for sticking with his Japanese club after they were forced to drop out of the league last year, as Hino Red Dolphins lifted the Division Three title with a 59-41 win over a Kurita Water Gush Akishima side coached by another ex-Wallaby, backrower Wycliff Palu.
