Both the #16 ARTA Honda of Nirei Fukuzumi and Hiroki Otsu and #100 Team Kunimitsu car of Naoki Yamamoto and Tadasuke Makino had 40 seconds added to their race times for illegally refuelling and changing tyres at the same time.
Fukuzumi and Otsu drop from second to third as a result, while Yamamoto and Makino slip to sixth position in the revised results.
It means that Nakajima Racing Honda moves up to second place, with Takuya Izawa and Kakunoshin Ota delivering the Dunlop-shod team its first podium finish for almost three years.
TOM'S Toyota pair Sho Tsuboi and Ritomo Miyata, who had led the standings heading into the Fuji race, move up from fifth to fourth at the expense of the Kunimitsu Honda.
That brings them within five points of new championship leaders Katsumasa Chiyo and Mitsunori Takaboshi, who claimed a dominant win aboard the NDDP Racing Nissan in the mixed conditions.
Cerumo Toyota pair Hiroaki Ishiura and Yuji Tachikawa meanwhile move up to fifth place.
In the GT300 class, the LM Corsa Toyota Supra of Hiroki Yoshimoto and Shunsuke Kohno was handed a 40-second penalty following Yoshimoto's final-turn contact with the works Subaru BRZ, dropping the car from fourth to 10th.
Yoshimoto had been battling the Subaru of Hideki Yamauchi on the last lap when he tagged the rear of his opponent and sent Yamauchi into a spin, an incident that dropped the Subaru to seventh at the finish.
The Kondo Racing Nissan of Joao Paulo de Oliveira and Teppei Natori moves up to fourth place as a result, ahead of the apr Lexus LC500h and the Subaru shared by Yamauchi and Takuto Iguchi.
De Oliveira and Natori therefore close to within two points of Seiji Ara, who leads the championship after finishing second in the Team Studie BMW M4 GT3 at Fuji alongside Masataka Yanagida.
Revised GT500 results:
1. #3 Niterra MOTUL Z
2. #64 Modulo NSX-GT
3. #16 ARTA MUGEN NSX-GT
4. #36 au TOM'S GR Supra
5. #38 ZENT CERUMO GR Supra
6. #100 STANLEY NSX-GT
7. #17 Astemo NSX-GT
8. #37 Deloitte TOM'S GR Supra
9. #39 DENSO KOBELCO SARD GR Supra
10. #24 Realize Corporation ADVAN Z
11. #14 ENEOS X PRIME GR Supra
12. #19 WedsSport ADVAN GR Supra
13. #23 MOTUL AUTECH Z
14. #8 ARTA MUGEN NSX-GT
15. #1 MARELLI IMPUL Z
Revised GT300 results:
1. #11 GAINER TANAX GT-R
2. #7 Studie BMW M4
3. #6 DOBOT Audi R8 LMS
4. #56 Realize Nissan Mechanic Challenge GT-R
5. #31 apr LC500h GT
6. #61 SUBARU BRZ R＆D SPORT
7. #10 PONOS GAINER GT-R
8. #88 JLOC Lamborghini GT3
9. #52 Saitama Toyopet GB GR Supra GT
10. #60 Syntium LMcorsa GR Supra GT
11. #2 muta Racing GR86 GT
12. #4 Goodsmile Hatsune Miku AMG
13. #30 apr GR86 GT
14. #360 RUNUP RIVAUX GT-R
15. #20 Shade Racing GR86 GT
16. #87 Bamboo Airways Lamborghini GT3
17. #18 UPGARAGE NSX GT3
18. #5 Mach Syaken Air Buster MC86
19. #50 ANEST IWATA Racing RC F GT3
20. #27 Yogibo NSX GT3
21. #48 Shokumou K's Frontier GT-R
22. #9 PACIFIC Vspo NAC AMG
23. #96 K-tunes RC F GT3
24. #22 R Q's AMG GT3
25. #65 LEON PYRAMID AMG
26. #25 HOPPY Schatz GR Supra GT
27. #244 HACHI-ICHI GR Supra GT
