Tsuboi and Miyata carved their way through from 12th on the grid to score their second win of 2023 aboard the #36 Toyota GR Supra and take a seven-point lead in the championship with only the season finale left to run.
In a thrilling and unpredictable 450km race, Miyata caught the long-time leading ARTA Honda of Hiroki Otsu in the closing stint of the race, with the pair engaging in a fierce duel for the top spot.
Otsu had taken over from team-mate Nirei Fukuzumi in the #16 ARTA NSX-GT on lap 59 of 97, while Miyata - who replaced Tsuboi at the wheel of the #36 car at the first round of pitstops - made his final stop on lap 65.
But Miyata fought through from a net fifth place to grab second within a matter of laps, dispatching the points-leading NDDP Racing Nissan of Mitsunori Takaboshi in the process, before closing down Otsu's five-second lead.
By lap 80, Miyata had caught up to the back of Otsu, and after several laps of on-the-limit dicing through the traffic, Miyata made the decisive move up the inside at the Turn 11 hairpin on lap 87.
Miyata went on to take the chequered flag by five seconds, as Otsu held off the NDDP Nissan that Takaboshi took over for the final stint from Katsumasa Chiyo.
The result means that the top three cars in the race are the only cars that can still win the championship in the season finale at Motegi: Fukuzumi and Otsu will head to the finale as rank outsiders in third, 13 points behind Tsuboi and Miyata with 21 on offer.
The Cerumo Toyota of Yuji Tachikawa and Hiroakj Ishiura was fourth after Ishiura made a late pass on the Impul Nissan of Kazuki Hiramine.
The Impul car shared by Hiramine and Bertrand Baguette made up ground from 13th on the grid with an undercut strategy, but fifth place marks the end of their title defence.
Honda squad Real Racing had looked to be in the frame for a podium finish late on, but Koudai Tsukakoshi faded late on to finish sixth in the NSX-GT started by Nobuharu Matsushita.
Next up were two more Toyota squads, the #37 TOM'S car of Ukyo Sasahara and Giuliano Alesi and the Rookie Racing machine of Kazuya Oshima and Kenta Yamashita.
Naoki Yamamoto's stand-in at Team Kunimitsu, Iori Kimura, brought home the NSX-GT he shared with Tadasuke Makino in ninth.
NISMO opted for an unconventional three-stop strategy for the Z shared by Ronnie Quintarelli and Tsugio Matsuda, but it failed to pay dividends and the duo had to be content with 10th.
The #8 ARTA Honda was a non-finisher after Tomoki Nojiri went off into the barriers in his stint, while the SARD Toyota was ruled out by mechanical issues.
A nailbiting GT300 contest was won by Saitama Toyopet Toyota GR Supra pairing Hiroki Yoshida and Kohta Kawaai, as Yoshida held off the Inging Toyota GR86 GT of Yuui Tsutsumi and Hibiki Taira by just 0.6s.
Yoshida and Kawaai's second straight win puts them on the cusp of the championship, as they lead with 20 points - Tsutsumi and Taira would need to score the maximum 21 points and hope their rivals fail to score to overhaul them.
Behind the leading two cars, the new apr Lexus LC500h scored its first podium finish in the hands of Kazuto Kotaka and Yuki Nemoto, who gamely held off the works Subaru BRZ of Takuto Iguchi in the closing stages.
Nemoto ensured a podium lockout for Toyota models and Bridgestone tyres in the process, while the Subaru crew of Iguchi and Hideki Yamauchi made it an-all JAF GT300 top four.
Best of the FIA GT3 finishers was the Kondo Racing Nissan GT-R NISMO GT3 of Teppei Natori and Joao Paulo de Oliveira, who made only one tyre change en route to an impressive recovery from 17th to fifth.
That result wasn't enough however to keep Natori and de Oliveira in title contention, with Team Studie BMW man Seiji Ara likewise dropping out of the running after finishing eighth in the M4 GT3 he shared with Bruno Spengler.
The UpGarage Honda team that was second in the points heading to Autopolis was taken out of the race by the K-tunes Racing Lexus RC F GT3, as Morio Nitta locked up and clouted the rear of Shun Koide's NSX GT3 at Turn 1.
Koide and Takashi Kobayashi were able to continue but finished down in 17th place.
GT500 results:
1. #36 au TOM'S GR Supra
2. #16 ARTA MUGEN NSX-GT
3. #3 Niterra MOTUL Z
4. #38 ZENT CERUMO GR Supra
5. #1 MARELLI IMPUL Z
6. #17 Astemo NSX-GT
7. #37 Deloitte TOM'S GR Supra
8. #14 ENEOS X PRIME GR Supra
9. #100 STANLEY NSX-GT
10. #23 MOTUL AUTECH Z
11. #64 Modulo NSX-GT
12. #24 Realize Corporation ADVAN Z
13. #19 WedsSport ADVAN GR Supra
DNF #39 DENSO KOBELCO SARD GR Supra
DNF #8 ARTA MUGEN NSX-GT
GT300 results:
1. #52 Saitama Toyopet GB GR Supra GT
2. #2 muta Racing GR86 GT
3. #31 apr LC500h GT
4. #61 SUBARU BRZ R＆D SPORT
5. #56 Realize Nissan Mechanic Challenge GT-R
6. #4 Goodsmile Hatsune Miku AMG
7. #88 JLOC Lamborghini GT3
8. #7 Studie BMW M4
9. #11 GAINER TANAX GT-R
10. #10 PONOS GAINER GT-R
11. #50 ANEST IWATA Racing RC F GT3
12. #65 LEON PYRAMID AMG
13. #20 Shade Racing GR86 GT
14. #360 RUNUP RIVAUX GT-R
15. #6 DOBOT Audi R8 LMS
16. #30 apr GR86 GT
17. #18 UPGARAGE NSX GT3
18. #5 Mach Syaken Air Buster MC86
19. #87 Bamboo Airways Lamborghini GT3
20. #60 Syntium LMcorsa GR Supra GT
21. #22 R'Qs AMG GT3
22. #48 Shokumou K's Frontier GT-R
23. #9 PACIFIC VSpo NAC AMG
DNF #27 Yogibo NSX GT3
DNF #96 K-tunes RC F GT3
