One-time Formula 1 champion Jenson Button resisted a determined drive from Ryo Hirakawa late on to seal the Super GT title for himself and team-mate Naoki Yamamoto.
Kunimitsu Racing pair Button and Yamamoto had to finish ahead of the #1 TOM'S Lexus LC500 shared by Hirakawa and Nick Cassidy to win the title, and did so by taking third place, just 1.5 seconds ahead of their main rivals.
It marks Honda's first Super GT title since 2010, with Button becoming the first rookie to win the title since Toranosuke Takagi achieved the feat in '05.
Yamamoto, who won the Super Formula title last month at Suzuka, also becomes the first driver to complete a clean sweep of titles in Japan's two most prestigious series since Richard Lyons in 2004.
However, The race was won by ARTA Honda pair Takuya Izawa and Tomoki Nojiri from pole, with Cerumo Lexus pair Hiroaki Ishiura and Yuji Tachikawa finishing second, 1.8s down at the finish.
Izawa led away at the start from pole as Yamamoto held second, while Cassidy made up one place on the opening lap to move into fifth behind Bertrand Baguette in the #64 Nakajima Honda and Tachikawa's #38 Cerumo Lexus.
That was how the order remained at the front until Izawa pitted the #8 NSX-GT from the lead to hand over to Nojiri on lap 19 of 53, at which point Yamamoto assumed control of the race.
Cassidy took second as Baguette and Tachikawa pitted to hand over to respective team-mates Kosuke Matsuura and Ishiura, and both Cassidy and race leader Yamamoto hit the pitlane together at the end of lap 29.
Button, taking over from Yamamoto, filtered back into fourth place, albeit quickly picking off Matsuura.
But the Englishman was unable to find a way by Ishiura, who did Lexus stablemates Cassidy and Hirakawa a huge favour by holding off Button's #100 NSX-GT for several laps.
In that time, Hirakawa was able to climb from eighth up to fourth, brusquely passing a fading Matsuura, and quickly set about closing the seven-second gap between himself and Button ahead.
Within three laps, he had cut the deficit to less than two seconds, and with five laps to go he was right on Button's tail.
The gap between Button and Hirakawa ebbed and flowed as the pair tried to negotiate slower GT300 traffic, but Button was able to score a decisive break on the penultimate lap and begin the final tour with 1.5s in hand.
That was enough for him to bring home the #100 Honda ahead of the #1 Lexus and secure the title.
Six seconds further ahead, Nojiri was able to manage his advantage over Ishiura's Lexus to claim a second victory of the season for himself and ARTA Honda teammate Izawa.
Completing the top five was the #19 WedsSport Lexus shared by Yuji Kunimoto and Kenta Yamashita, ahead of the #6 Team LeMans Lexus of Kazuya Oshima and Felix Rosenqvist.
Nissan's top finisher was the #23 NISMO GT-R of Tsugio Matsuda and Ronnie Quintarelli in seventh.
Baguette and Matsuura ended up down in 12th after the latter was hit from behind by the #38 TOM'S Lexus of outside title contender Yuki Sekiguchi.
Izawa and Nojiri's victory moved them up to third in the final points ahead of Sekiguchi, who failed to score in 13th.