| 1st | 8 | Katsutomo Kaneishi / Keiichi Tsuchiya | Honda NSX (GH-NA2) | Autobacs Racing Team Aguri | 1:58.2900 |
| 2nd | 1 | Ryou Michigami / Hidetoshi Mitsusada | Honda NSX (GH-NA2) | Dome Mugen Project | 1:58.5280 |
| 3rd | 18 | Sébastien Philippe / Benoit Tréluyer | Honda NSX (GH-NA2) | Dome Mugen Project | 1:59.0350 |
| 4th | 12 | Kazuyoshi Hoshino / Satoshi Motoyama | Nissan Skyline GT-R (BNR34) | Team Impul | 1:59.1950 |
| 5th | 39 | Jeremie Dufour / Romain Dumas | Toyota Supra (JZA80) | Toyota Team SARD | 1:59.2490 |
| 6th | 30 | Hideki Okada / André Couto | McLaren F1 GTR (4S70) | Team Take One | 1:59.2920 |
| 7th | 6 | Juichi Wakisaka / Hideki Noda | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:59.3270 |
| 8th | 22 | Michael Krumm / Tetsuya Tanaka | Nissan Skyline GT-R (BNR34) | NISMO | 1:59.3330 |
| 9th | 100 | Akira Iida / Daisuke Itou | Honda NSX (GH-NA2) | Team Kunimitsu With Mooncraft | 1:59.3340 |
| 10th | 37 | Shin'ichi Yamaji / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:59.3370 |
| 11th | 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:59.3770 |
| 12th | 23 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:59.4200 |
| 13th | 25 | Manabu Orido / Seiji Ara | Toyota Supra (JZA80) | Tsuchiya Engineering | 1:59.4890 |
| 14th | 36 | Takuya Kurosawa / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Team Tom's | 1:59.5140 |
| 15th | 21 | Naoki Hattori / Akihiko Nakaya | McLaren F1 GTR (4S70) | Hitotsuyama Racing | 1:59.5520 |
| 16th | 64 | Tsugio Matsuda / Dominik Schwager | Honda NSX (GH-NA2) | Mobil1 Nakajima Racing | 1:59.6020 |
| 17th | 33 | Ukyou Katayama / Masahiko Kondou | Toyota Supra (JZA80) | Toyota Team Cerumo With Ukyo | 2:01.1600 |
| 18th | 88 | Naohiro Furuya / Marco Apicella | Lamborghini Diablo (DE21) | JLOC | 2:03.6640 |
| 19th | 81 | Takayuki Aoki / Nobuyuki Ohyagi | Nissan Silvia (S15) | Team Daishin | 2:10.1580 |
| 20th | 0 | Masahiro Matsunaga / Kumi Satou | Toyota MR-S (GH-ZZW30) | Tom's Spilit | 2:10.2850 |
| 21st | 7 | Haruhiko Matsumoto / Tetsuya Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:10.2940 |
| 22nd | 3 | Yuuji Ide / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 2:10.3330 |
| 23rd | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (GH-ZZW30) | ARTA With A'pex | 2:10.3810 |
| 24th | 71 | Masaki Jounai / Eiichi Tajima | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 2:10.8500 |
| 25th | 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | KRAFT | 2:10.8730 |
| 26th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 2:10.9270 |
| 27th | 11 | Jun'ichi Ikura / Yuusei Maki | Porsche 996 GT3-R | Team Gainer | 2:11.4710 |
| 28th | 62 | Shinsuke Shibahara / Shogo Mitsuyama | Porsche 996 GT3-R | R&D Sport | 2:11.8020 |
| 29th | 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D Sport | 2:11.9080 |
| 30th | 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (GH-ZZW30) | Racing Project Bandoh | 2:11.9310 |
| 31st | 360 | Kota Sasaki / Seigou Nishizawa | Ferrari 360 Modena (GFF360) | Dentaire Projet | 2:12.0400 |
| 32nd | 24 | Hideshi Matsuda / Kazuyuki Nishizawa | Porsche 996 GT3-R | Team Taisan Advan | 2:12.1920 |
| 33rd | 910 | Hisashi Wada / Tomohiko Sunako | Porsche 996 GT3-RS | 910 Racing | 2:12.6840 |
| 34th | 26 | Hideo Fukuyama / Atsushi Yogou | Porsche 996 GT3-RS | Team Taisan Advan | 2:13.0730 |
| 35th | 51 | Naofumi Omoto / Yasukichi Yamamoto | Nissan Silvia (S15) | Auto Staff Racing Team | 2:13.2530 |
| 36th | 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Dream 28 | 2:14.9820 |
| 37th | 901 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 2:15.0900 |
| 38th | 70 | Yoshimi Ishibashi / Hiroaki Suga | Porsche 996 GT3-RS | Team Gaikokuya | 2:15.5210 |
| 39th | 9 | Yousuke Shimojima / Tsunefumi Hioki | Porsche 996 GT3-R | Team Daikokuya | 2:13.2620 |