| 1st | 64 | Tsugio Matsuda / Dominik Schwager | Honda NSX (GH-NA2) | Mobil1 Nakajima Racing | 1:47.5750 |
| 2nd | 30 | Hideki Okada / André Couto | McLaren F1 GTR (4S70) | Team Take One | 1:47.7570 |
| 3rd | 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:47.8380 |
| 4th | 25 | Manabu Orido / Seiji Ara | Toyota Supra (JZA80) | Tsuchiya Engineering | 1:47.9170 |
| 5th | 12 | Kazuyoshi Hoshino / Satoshi Motoyama | Nissan Skyline GT-R (BNR34) | Team Impul | 1:48.3270 |
| 6th | 21 | Naoki Hattori / Akihiko Nakaya | McLaren F1 GTR (4S70) | Hitotsuyama Racing | 1:48.4960 |
| 7th | 39 | Jeremie Dufour / Romain Dumas | Toyota Supra (JZA80) | Toyota Team SARD | 1:48.5090 |
| 8th | 100 | Akira Iida / Daisuke Itou | Honda NSX (GH-NA2) | Team Kunimitsu With Mooncraft | 1:48.5170 |
| 9th | 6 | Juichi Wakisaka / Hideki Noda | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:48.5630 |
| 10th | 18 | Sébastien Philippe / Benoit Tréluyer | Honda NSX (GH-NA2) | Dome Mugen Project | 1:48.5830 |
| 11th | 22 | Michael Krumm / Tetsuya Tanaka | Nissan Skyline GT-R (BNR34) | NISMO | 1:48.6540 |
| 12th | 1 | Ryou Michigami / Hidetoshi Mitsusada | Honda NSX (GH-NA2) | Dome Mugen Project | 1:48.6900 |
| 13th | 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (GH-NA2) | Autobacs Racing Team Aguri | 1:48.8590 |
| 14th | 36 | Takeshi Tsuchiya / Paolo Montin | Toyota Supra (JZA80) | Toyota Team Tom's | 1:49.0710 |
| 15th | 23 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:49.2350 |
| 16th | 33 | Shigekazu Wakisaka / Masahiko Kondou | Toyota Supra (JZA80) | Toyota Team Cerumo With Ukyo | 1:49.3470 |
| 17th | 37 | Shin'ichi Yamaji / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:49.6860 |
| 18th | 88 | Naohiro Furuya / Marco Apicella | Lamborghini Diablo (DE21) | JLOC | 1:52.7140 |
| 19th | 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (GH-ZZW30) | Racing Project Bandoh | 1:57.5190 |
| 20th | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:58.0470 |
| 21st | 3 | Yuuji Ide / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 1:58.5700 |
| 22nd | 7 | Haruhiko Matsumoto / Tetsuya Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:58.7490 |
| 23rd | 26 | Hideo Fukuyama / Atsushi Yogou | Porsche 996 GT3-RS | Team Taisan Advan | 1:58.8430 |
| 24th | 71 | Masaki Jounai / Eiichi Tajima | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 1:58.8470 |
| 25th | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (GH-ZZW30) | ARTA With A'pex | 1:58.9130 |
| 26th | 24 | Hideshi Matsuda / Kazuyuki Nishizawa | Porsche 996 GT3-R | Team Taisan Advan | 1:58.9590 |
| 27th | 55 | Eiji Yamada / Takayuki Kinoshita | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 1:59.0700 |
| 28th | 62 | Shinsuke Shibahara / Shogo Mitsuyama | Porsche 996 GT3-R | R&D Sport | 1:59.0780 |
| 29th | 360 | Kota Sasaki / Seigou Nishizawa | Ferrari 360 Modena (GFF360) | Dentaire Projet | 1:59.3220 |
| 30th | 11 | Jun'ichi Ikura / Yuusei Maki | Porsche 996 GT3-R | Team Gainer | 1:59.3760 |
| 31st | 51 | Naofumi Omoto / Yasukichi Yamamoto | Nissan Silvia (S15) | Auto Staff Racing Team | 1:59.6610 |
| 32nd | 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D SPORT | 1:59.7020 |
| 33rd | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 1:59.7470 |
| 34th | 9 | Akira Watanabe / Tsunefumi Hioki | Porsche 996 GT3-R | Team Daikokuya | 1:59.7920 |
| 35th | 910 | Hisashi Wada / Tomohiko Sunako | Porsche 996 GT3-RS | 910 Racing | 1:59.9090 |
| 36th | 901 | Takeshi Asami / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 2:00.3680 |
| 37th | 0 | Masahiro Matsunaga / Kumi Satou | Toyota MR-S (GH-ZZW30) | Tom's Spilit | 2:01.0120 |
| 38th | 70 | Yoshimi Ishibashi / Hiroaki Suga | Porsche 996 GT3-RS | Team Gaikokuya | 2:01.3000 |
| 39th | 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | KRAFT | 2:01.3600 |
| 40th | 2 | Kazuho Takahashi / Hiroshi Kimura | Honda NSX (GH-NA2) | Dream 28 | 2:02.2800 |