| 1st | 18 | Juichi Wakisaka / Katsutomo Kaneishi | Honda NSX (GH-NA2) | Dome Mugen Project | 1:46.9680 |
| 2nd | 16 | Osamu Nakako / Ryou Michigami | Honda NSX (GH-NA2) | Dome Mugen Project | 1:48.4420 |
| 3rd | 100 | Akira Iida / Naoki Hattori | Honda NSX (GH-NA2) | Team Kunimitsu With Mooncraft | 1:48.4620 |
| 4th | 1 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:48.6000 |
| 5th | 12 | Kazuyoshi Hoshino / Satoshi Motoyama | Nissan Skyline GT-R (BNR34) | Team Impul | 1:49.0440 |
| 6th | 30 | Youji Yamada / Hideki Okada | McLaren F1 GTR | Team Take One | 1:49.1340 |
| 7th | 3 | Masahiro Hasemi / Tetsuya Tanaka | Nissan Skyline GT-R (BNR34) | Hasemi Motorsports | 1:49.1520 |
| 8th | 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:49.3590 |
| 9th | 36 | Masanori Sekiya / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Castrol Team Tom's | 1:49.4370 |
| 10th | 8 | Aguri Suzuki / Keiichi Tsuchiya | Honda NSX (E-NA2) | Autobacs Racing Team Aguri | 1:49.4480 |
| 11th | 32 | Takayuki Kinoshita / Masahiko Kondou | Toyota Supra (JZA80) | cdma One Toyota Team Cerumo With Key's | 1:49.4660 |
| 12th | 6 | Hideki Noda / Wayne Gardner | Toyota Supra (JZA80) | Esso Ultron Toyota Team Le Mans | 1:49.5850 |
| 13th | 64 | Daisuke Itou / Dominik Schwager | Honda NSX (E-NA2) | Mobil1 Nakajima Racing | 1:49.8260 |
| 14th | 21 | Mikio Hitotsuyama / Akihiko Nakaya | McLaren F1 GTR | Hitotsuyama Racing | 1:50.2220 |
| 15th | 2 | Yuuji Ide / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:50.2420 |
| 16th | 37 | Seiji Ara / Toshio Suzuki | Toyota Supra (JZA80) | Toyota Castrol Team Tom's | 1:50.3850 |
| 17th | 39 | Masahiko Kageyama / Ralph Firman | Toyota Supra (JZA80) | Toyota Team SARD | 1:50.5310 |
| 18th | 35 | Shin'ichi Yamaji / Pierre-Henri Raphanel | Toyota Supra (JZA80) | Matsumotokiyoshi Team Tom's | 1:50.7080 |
| 19th | 25 | Mitsuhiro Kinoshita / Manabu Orido | Toyota Supra (JZA80) | Endless+Tsuchiya Engineering | 1:51.0690 |
| 20th | 88 | Naohiro Furuya / Tsuyoshi Takahashi | Lamborghini Diablo (ZA90DE068) | JLOC | 1:51.6050 |
| 21st | 55 | Hiroaki Suga / Shinsuke Shibahara | Chrysler Viper GTS-R | Team Taisan | 1:52.0440 |
| 22nd | 26 | Hideshi Matsuda / Hideo Fukuyama | Porsche 996 GT3-R | Team Taisan Jr. With Advan | 1:56.7330 |
| 23rd | 910 | Atsushi Yogou / Hisashi Wada | Porsche 996 GT3-R | 910 Racing | 1:57.0220 |
| 24th | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:57.3690 |
| 25th | 19 | Shigekazu Wakisaka / Takahiko Hara | Toyota Celica (ST205) | Racing Project Bandoh | 1:57.6100 |
| 26th | 7 | Haruhiko Matsumoto / Tetsuya Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:57.9920 |
| 27th | 911 | Masamitsu Ishihara / Tomohiko Sunako | Porsche 996 GT3-R | 910 Racing | 1:58.4420 |
| 28th | 31 | Morio Nitta / Yuudai Igarashi | Toyota MR-S (GH-ZZW30) | Super Autobacs A'pex MR-S | 1:59.1820 |
| 29th | 10 | Yasutaka Hinoi / Yutaka Yamagishi | Porsche 911 GT2 | Ability Motorsports | 1:59.9820 |
| 30th | 111 | Jun'ichi Ikura / Yuusei Maki | Ferrari F355 | Team Gainer | 2:01.7470 |
| 31st | 70 | Yoshimi Ishibashi / Patrick van Schoote | Porsche 911 GT2 | Team Gaikokuya | 2:03.1770 |
| 32nd | 27 | Kota Sasaki / Seigou Nishizawa | Porsche 993 RSR | Team Daikokuya | 2:04.3760 |
| 33rd | 9 | Syuuroku Sasaki / Tsunefumi Hioki | Porsche 993 RSR 3.8 | Team Daikokuya | 2:03.0020 |
| 34th | 24 | Kazuyuki Nishizawa / Marco Apicella | Porsche 986 Boxster | MTCI Racing Team | 2:06.2670 |
| 35th | 11 | Kengo Kitaura / Hikaru Miyagi | Porsche 911 RSR | Ability Motorsports | 2:33.0230 |