| 1st | 76 | Naoki Hattori / Eiichi Tajima | McLaren F1 GTR (19R GTR) | Hitotsuyama Racing | 1:46.7240 |
| 2nd | 36 | Takeshi Tsuchiya / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:46.8410 |
| 3rd | 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:46.8850 |
| 4th | 35 | Masahiko Kageyama / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:46.8930 |
| 5th | 18 | Sébastien Philippe / Richard Lyons | Honda NSX (LA-NA2) | Dome Mugen Project | 1:46.9260 |
| 6th | 16 | Ryou Michigami / Daisuke Itou | Honda NSX (LA-NA2) | Dome Mugen Project | 1:46.9560 |
| 7th | 64 | Tsugio Matsuda / Ralph Firman | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:46.9720 |
| 8th | 39 | Jeremie Dufour / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:47.1630 |
| 9th | 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:47.1650 |
| 10th | 25 | Seiji Ara / Shin'ichi Yamaji | Toyota Supra (JZA80) | Tsuchiya Engineering | 1:47.5670 |
| 11th | 23 | Masami Kageyama / Erik Comas | Nissan Skyline GT-R (BNR34) | NISMO | 1:47.6130 |
| 12th | 30 | Hideki Okada / Haruki Kurosawa | McLaren F1 GTR (19R GTR) | Team Take One | 1:47.6340 |
| 13th | 37 | Takuya Kurosawa / Paolo Montin | Toyota Supra (JZA80) | Toyota Team Tom's | 1:47.6560 |
| 14th | 33 | Masahiko Kondou / Hayanari Shimoda | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:48.1800 |
| 15th | 12 | Tetsuya Tanaka / Benoit Tréluyer | Nissan Skyline GT-R (BNR34) | Team Impul | 1:48.2120 |
| 16th | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:48.8020 |
| 17th | 22 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:48.8320 |
| 18th | 1 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:49.0620 |
| 19th | 88 | Marco Apicella / Hisashi Wada | Lamborghini Diablo JGT-1 (ZA90DE068) | JLOC | 1:52.1480 |
| 20th | 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 1:55.3880 |
| 21st | 26 | Atsushi Yogou / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan Advan | 1:55.8880 |
| 22nd | 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 1:55.9050 |
| 23rd | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 1:56.0270 |
| 24th | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (ZZW30) | ARTA With A'pex | 1:56.3260 |
| 25th | 7 | Haruhiko Matsumoto / Nobuteru Taniguchi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:56.4670 |
| 26th | 3 | Tetsuya Yamano / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 1:56.5430 |
| 27th | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:56.5920 |
| 28th | 28 | Yukihiro Hane / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Taisan Jr. | 1:56.8430 |
| 29th | 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (ZZW30) | Racing Project Bandoh | 1:56.8500 |
| 30th | 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (ZZW30) | KRAFT | 1:56.8670 |
| 31st | 71 | Masaki Jounai / Keita Sawa | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 1:56.8990 |
| 32nd | 910 | Hideshi Matsuda / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 1:57.1680 |
| 33rd | 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:57.2390 |
| 34th | 24 | Hideo Fukuyama / Mitsuhiro Kinoshita | Porsche 996 GT3-R | Team Taisan Advan | 1:57.2550 |
| 35th | 55 | Eiji Yamada / Gou Shimizu | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 1:57.4470 |
| 36th | 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 1:58.2170 |
| 37th | 21 | Mikio Hitotsuyama / Yasushi Kikuchi | BMW M3 GT (E46) | Hitotsuyama Racing | 1:58.4670 |
| 38th | 66 | Tetsuya Shimizu / Makoto Shionoiri | Mazda RX-7 (FD3S) | Team Revolution | 1:58.7000 |
| 39th | 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D Sport | 1:59.1050 |
| 40th | 911 | Akira Hirakawa / Shigemitsu Haga | Porsche 996 GT3-RS | 910 Racing | 1:59.3500 |
| 41st | 87 | Kouji Yamanishi / Yuudai Igarashi | Mercedes-Benz CLK (GF-208) | HKS | 1:59.7230 |
| 42nd | 70 | Yoshimi Ishibashi / Seiichi Sodeyama | Porsche 996 GT3-RS | Team Gaikokuya | 2:01.1680 |
| 43rd | 4 | Naohiro Furuya / Izumi Yoshida | Chevrolet Corvette (C-4) | Zipspeed | 2:11.9670 |