| 1st | 18 | Juichi Wakisaka / Katsutomo Kaneishi | Honda NSX (GH-NA2) | Dome Mugen Project | 1:34.6240 |
| 2nd | 64 | Daisuke Itou / Dominik Schwager | Honda NSX (GH-NA2) | Mobil1 Nakajima Racing | 1:34.7050 |
| 3rd | 16 | Ryou Michigami / Hidetoshi Mitsusada | Honda NSX (GH-NA2) | Dome Mugen Project | 1:35.1720 |
| 4th | 100 | Akira Iida / Naoki Hattori | Honda NSX (GH-NA2) | Team Kunimitsu With Mooncraft | 1:35.1880 |
| 5th | 12 | Kazuyoshi Hoshino / Satoshi Motoyama | Nissan Skyline GT-R (BNR34) | Team Impul | 1:35.3040 |
| 6th | 1 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:35.4380 |
| 7th | 8 | Aguri Suzuki / Keiichi Tsuchiya | Honda NSX (GH-NA2) | Autobacs Racing Team Aguri | 1:35.5520 |
| 8th | 2 | Ukyou Katayama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:35.7950 |
| 9th | 35 | Shin'ichi Yamaji / Pierre-Henri Raphanel | Toyota Supra (JZA80) | Matsumotokiyoshi Team Tom's | 1:36.0820 |
| 10th | 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:36.2800 |
| 11th | 6 | Hideki Noda / Wayne Gardner | Toyota Supra (JZA80) | Esso Ultron Toyota Team Le Mans | 1:36.4780 |
| 12th | 36 | Masanori Sekiya / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Castrol Team Tom's | 1:36.8540 |
| 13th | 39 | Masahiko Kageyama / Ralph Firman | Toyota Supra (JZA80) | Toyota Team SARD | 1:37.5390 |
| 14th | 30 | Hideki Okada / Tsugio Matsuda | McLaren F1 GTR | Team Take One | 1:37.7000 |
| 15th | 37 | Seiji Ara / Toshio Suzuki | Toyota Supra (JZA80) | Toyota Castrol Team Tom's | 1:38.0830 |
| 16th | 21 | Mikio Hitotsuyama / Akihiko Nakaya | McLaren F1 GTR | Hitotsuyama Racing | 1:38.6580 |
| 17th | 25 | Mitsuhiro Kinoshita / Manabu Orido | Toyota Supra (JZA80) | Endless+Tsuchiya Engineering | 1:38.7730 |
| 18th | 32 | Takayuki Kinoshita / Masahiko Kondou | Toyota Supra (JZA80) | cdma One Toyota Team Cerumo With Key's | 1:39.1060 |
| 19th | 3 | Masahiro Hasemi / Tetsuya Tanaka | Nissan Skyline GT-R (BNR34) | Hasemi Motorsports | 1:41.1140 |
| 20th | 88 | Naohiro Furuya / Tsuyoshi Takahashi | Lamborghini Diablo (ZA90DE068) | JLOC | 1:42.5460 |
| 21st | 28 | Hiroaki Suga / Shinsuke Shibahara | Porsche 996 GT3-R | Team Taisan Jr. With Advan | 1:39.1680 |
| 22nd | 7 | Haruhiko Matsumoto / Tetsuya Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:40.3950 |
| 23rd | 11 | Jun Kinoshita / Yasutaka Hinoi | Porsche 911 GT2 | Ability Motorsports | 1:40.8810 |
| 24th | 26 | Hideshi Matsuda / Hideo Fukuyama | Porsche 996 GT3-R | Team Taisan Jr. With Advan | 1:41.1820 |
| 25th | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (GH-ZZW30) | Super Autobacs Racing TeamWith A'pex | 1:41.5540 |
| 26th | 55 | Eiji Yamada / Takahide Tasaki | Chrysler Viper GTS-R | Team Taisan Advan | 1:42.0660 |
| 27th | 910 | Atsushi Yogou / Hisashi Wada | Porsche 996 GT3-R | 910 Racing | 1:42.0680 |
| 28th | 24 | Kazuyuki Nishizawa / Marco Apicella | Porsche 986 Boxster | Sport Today Racing Team | 1:42.3330 |
| 29th | 19 | Shigekazu Wakisaka / Takahiko Hara | Toyota Celica (ST205) | Racing Project Bandoh | 1:43.3350 |
| 30th | 71 | Masaki Jounai / Masanobu Takenaka | Porsche 911 GT2 | Sigmatech Racing Team | 1:43.7970 |
| 31st | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:44.1140 |
| 32nd | 51 | Seiichi Sodeyama / Naofumi Omoto | Nissan Silvia (S14) | Auto Staff Racing Team | 1:44.9580 |
| 33rd | 20 | Masahiro Matsunaga / Kumi Satou | Toyota MR-S (GH-ZZW30) | Tom's Spilit | 1:45.1870 |
| 34th | 70 | Yoshimi Ishibashi / Nobuo Komiya | Porsche 911 GT2 | Team Gaikokuya | 1:45.4490 |
| 35th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GC8) | Cusco Racing | 1:45.9760 |
| 36th | 86 | Minoru Tanaka / Kouji Matsuda | Toyota Trueno (AE86) | Kraft | 1:46.3340 |