B-Max pair Frederic Makowiecki and Kohei Hirate delivered Nissan's first 2019 SUPER GT win in a rain-hit race at Sugo as early leaders Jenson Button and Naoki Yamamoto finished eighth.
As the race got under way after three laps behind the safety car, front-row starter Button immediately sprinted past polesitter Koudai Tsukakoshi into Turn 1, aided by Real Racing's ill-judged decision to start on slick tyres.
Button was followed by the TOM'S Lexus of Nick Cassidy and the two drivers initially ran nose-to-tail, before the leader stretched out an advantage that peaked at 10 seconds.
The 2009 Formula 1 champion handed over the Kunimitsu Honda to team-mate Yamamoto on lap 36 of 81, nine laps after Cassidy made his stop and passed on the baton to Ryo Hirakawa.
Yamamoto struggled on cold tyres after the pitstop, allowing Hirakawa to rapidly close in on him and overtake even before Yamamoto had completed his out-lap.
The pass was perfectly timed as the safety car was deployed almost immediately afterwards to allow the Impul Nissan, which was beached at Turn 2, to be retrieved.
At the restart, Hirakawa pulled away from Yamamoto - who appeared to struggle further as the conditions worsened and started falling down the order.
At the same time, Makowiecki started charging up the pack in the Michelin-shod B-Max Nissan, repassing the NISMO Nissan of Tsugio Matsuda before dispatching the points-leading LeMans Lexus and the struggling Honda of Yamamoto in quick succession.
By lap 53, Makowiecki had Hirakawa in his sights and on the following lap, the SUPER GT returnee made a brave pass around the outside of Turn 1 to snatch the lead of the race.
From there on, Makowiecki cruised to the finish, scoring a first win for Nissan since last year's Fuji 500-mile round.
Formula 2 race winner Tadasuke Makino likewise thrived in the difficult wet conditions, charging through the field in the second half of the race to finish second in the Nakajima Honda he shares with Narain Karthikeyan.
It marked the first podium finish for the Satoru Nakajima-led team since it won the last running of the Suzuka 1000km in 2017.
Matsuda and Ronnie Quintarelli finished third in the NISMO GT-R, completing a double podium finish for Nissan.
Hirakawa held on to fourth place in the #37 TOM'S Lexus he shares with Cassidy, albeit over 40s down on race winners Makowiecki and Hirate.
Real Racing Honda duo Tsukakoshi and Bertrand Baguette were next up in fifth, recovering from the costly tyre choice error that left them towards the back of the pack in the early stages.
Kenta Yamashita and Kazuya Oshima finished sixth in the LeMans Lexus, ensuring they head into the season finale at Motegi with a seven-point lead over Cassidy and Hirakawa.
Autopolis winners Heikki Kovalainen and Yuichi Nakayama finished seventh in the SARD Lexus, while Button and Yamamoto were eventually classified a disappointing eighth after the latter had to come into the pits for a second stop.