NDDP pair Katsumasa Chiyo and Mitsunori Takaboshi looked on course for a commanding victory from pole in the #3 Nissan Z for much of the race, but the arrival of rain in the closing stages opened the door for a late twist in the title battle.
Miyata was running in second, around 10 seconds behind Takaboshi, with a similar margin over the third-placed NISMO Nissan of Tsugio Matsuda, when the conditions started to deteriorate.
With a seven-point gap in hand over the NDDP Nissan crew, Miyata only needed to bring the car home in second to guarantee himself and Tsuboi the title, and closed in on Takaboshi as the leaders started circulating up to 15s a lap off the pace.
The gap was down to around five seconds when Takaboshi made a crucial error on lap 59 of 63 and spun his Nissan at the Turn 8 right-hander, ending up beached in the gravel.
That allowed Miyata to take the lead, which he held to the chequered flag by five seconds over the NISMO Nissan of Tsugio Matsuda and Ronnie Quintarelli, bagging a first title for himself and a second for Tsuboi.
The third win of the season meant that the #36 TOM'S crew finished 26 points clear of Chiyo and Takaboshi in the final championship standings.
Miyata became only the fifth driver in history to claim a double of titles in Super Formula and SUPER GT in the same year.
Completing the podium was the #17 Real Racing Honda NSX-GT of Koudai Tsukakoshi and Nobuharu Matsushita, which was among a minority of cars to change to wet tyres in the closing stages but lacked the pace to catch the leading two cars.
Tsukakoshi passed Matsuda in a thrilling fight for third on lap 53, but surrendered the place by pitting on lap 57 to change to wets, and while the gamble looked like it could pay off initially, the rain wasn't heavy enough to allow Tsukakoshi to close the gap.
He and Matsushita finally fell 16s short of delivering Honda a farewell win for the NSX-GT.
Fourth place went to outgoing champions Bertrand Baguette and Kazuki Hiramine in the Impul Nissan, while ARTA Honda duo Tomoki Nojiri and Toshiki Oyu wrapped a tumultous season with a smooth run to fifth in the #8 NSX-GT.
The sister #16 ARTA car of Nirei Fukuzumi and Hiroki Otsu, who entered the race with slim title aspirations, ended up 12th after also changing to wet tyres in the latter stages.
That meant they were beaten to third in the championship by Quintarelli and Matsuda by three points.
Rookie Racing Toyota duo Kenta Yamashita and Kazuya Oshima finished sixth despite Oshima being turned around by the Kunimitsu Honda of Iori Kimura in an early battle for fifth position.
Kimura was handed a drive-through penalty for the offence, limiting he and Tadasuke Makino to the final points position in 10th.
Yuji Tachikawa wrapped up his illustrious GT500 career in 11th place alongside Cerumo Toyota team-mate Hiroaki Ishiura, while Chiyo and Takaboshi were finally classified 13th.
GT300: Saitama Toyopet pair hang on for title
GT300 title honours went to Saitama Toyopet Toyota pair Hiroki Yoshida and Kohta Kawaai, who needed only a single point to wrap up the title and finished seventh in the treacherous conditions.
Victory in the final race went to JLOC Lamborghini duo Takashi Kogure and Yuya Motojima, who beat LEON Racing Mercedes pair Naoya Gamou and Takuro Shinohara by seven seconds.
Both the JLOC and LEON cars trailed the pole-winning Inging Toyota GR86 GT in the early stages, with Hibiki Taira and Yuui Tsutsumi needing to win the race to have any hope of taking the title away from Saitama Toyopet.
But Motojima managed to put a move on Taira even before the pitstop phase began to set up a first JLOC win since 2019, and a first for the new Evo2 Huracan GT3 that was introduced mid-season.
The Inging squad also found itself undercut by the early-stopping LEON Mercedes AMG GT3, and was running third when the team gambled on putting Tsutsumi on wet tyres late on.
That left Taira and Tsutsumi down in ninth at the finish, as Yoshida completed a nervy final few laps to grab the single point he and Kawaai needed to take the title at their fourth attempt as a duo.
Ex-Formula 1 driver Roberto Merhi concluded his second SUPER GT season with podium in the Team LeMans Audi R8 LMS GT3 he shares with Yoshiaki Katayama, just ahead of the apr Lexus LC500h of Kazuto Kotaka and Yuki Nemoto.
Kondo Racing Nissan duo Joao Paulo de Oliveira and Teppei Natori came back from virtually last on the grid to claim sixth place, gambling on not changing tyres during the race.
That result was enough to give de Oliveira and Natori third in the overall standings, with the LEON Mercedes fourth and the UpGarage Honda NSX GT3 that finished eighth claiming the final place in the top five overall.
Race results:
GT500
1. #36 au TOM'S GR Supra 63 laps
2. #23 MOTUL AUTECH Z +5.159
3. #17 Astemo NSX-GT +16.270
4. #1 MARELLI IMPUL Z +30.349
5. #8 ARTA MUGEN NSX-GT +32.045
6. #14 ENEOS X PRIME GR Supra +46.456
7. #39 DENSO KOBELCO SARD GR Supra +51.864
8. #19 WedsSport ADVAN GR Supra +58.819
9. #37 Deloitte TOM'S GR Supra +1:02.089
10. #100 STANLEY NSX-GT +1:05.534
11. #38 ZENT CERUMO GR Supra +1:07.734
12. #16 ARTA MUGEN NSX-GT +1:11.295
13. #3 Niterra MOTUL Z +1:32.001
14. #24 Realize Corporation ADVAN Z +1lap
Ret. #64 Modulo NSX-GT
GT300
1. #88 JLOC Lamborghini GT3 59 laps
2. #65 LEON PYRAMID AMG +7.124
3. #6 DOBOT Audi R8 LMS +22.795
4. #31 apr LC500h GT +23.265
5. #96 K-tunes RC F GT3 +38.520
6. #56 Realize Nissan Mechanic Challenge GT-R +40.318
7. #52 Saitama Toyopet GB GR Supra GT +42.621
8. #18 UPGARAGE NSX GT3 +44.223
9. #2 muta Racing GR86 GT +51.049
10. #61 SUBARU BRZ R＆D SPORT +1:01.284
11. #4 Goodsmile Hatsune Miku AMG +1lap
12. #7 Studie BMW M4 +1lap
13. #11 GAINER TANAX GT-R +1lap
14. #20 Shade Racing GR86 GT +1lap
15. #60 Syntium LMcorsa GR Supra GT +1lap
16. #10 PONOS GAINER GT-R +1lap
17. #50 ANEST IWATA Racing RC F GT3 +1lap
18. #5 Mach Syaken Air Buster MC86 +1lap
19. #9 PACIFIC VSpo NAC AMG +2laps
20. #48 Shokumou K's Frontier GT-R +3laps
21. #87 Bamboo Airways Lamborghini GT3 +3laps
22. #22 R'Qs AMG GT3 +3laps
23. #30 apr GR86 GT +8laps
24. #360 RUNUP RIVAUX GT-R +12laps
Ret. #27 Yogibo NSX GT3
