| 1st | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:55.8100 |
| 2nd | 18 | Sébastien Philippe / Richard Lyons | Honda NSX (LA-NA2) | Dome Mugen Project | 1:56.0000 |
| 3rd | 37 | Takuya Kurosawa / Hideki Noda | Toyota Supra (JZA80) | Toyota Team Tom's | 1:56.3900 |
| 4th | 64 | Ralph Firman / Tsugio Matsuda | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:56.5190 |
| 5th | 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:56.5850 |
| 6th | 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:56.7270 |
| 7th | 39 | Jeremie Dufour / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:56.8990 |
| 8th | 16 | Ryou Michigami / Daisuke Itou | Honda NSX (LA-NA2) | Dome Mugen Project | 1:57.0710 |
| 9th | 1 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:57.2000 |
| 10th | 25 | Seiji Ara / Shin'ichi Yamaji | Toyota Supra (JZA80) | Tsuchiya Engineering | 1:57.2180 |
| 11th | 23 | Masami Kageyama / Erik Comas | Nissan Skyline GT-R (BNR34) | NISMO | 1:57.3350 |
| 12th | 36 | Takeshi Tsuchiya / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:57.3740 |
| 13th | 12 | Tetsuya Tanaka / Benoit Tréluyer | Nissan Skyline GT-R (BNR34) | Team Impul | 1:57.4720 |
| 14th | 22 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:57.8310 |
| 15th | 30 | Hideki Okada / Haruki Kurosawa | McLaren F1 GTR (19R GTR) | Team Take One | 1:57.9640 |
| 16th | 35 | Masahiko Kageyama / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:57.9650 |
| 17th | 76 | Naoki Hattori / Eiichi Tajima | McLaren F1 GTR (19R GTR) | Hitotsuyama Racing | 1:58.5800 |
| 18th | 33 | Masahiko Kondou / Hayanari Shimoda | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:58.8130 |
| 19th | 88 | Marco Apicella / Hisashi Wada | Lamborghini Diablo JGT-1 (ZA90DE068) | JLOC | 2:03.2050 |
| 20th | 87 | Kouji Yamanishi / Yuudai Igarashi | Mercedes-Benz CLK (GF-208) | HKS | 2:04.9910 |
| 21st | 71 | Masaki Jounai / Keita Sawa | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 2:07.3170 |
| 22nd | 3 | Tetsuya Yamano / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 2:07.6460 |
| 23rd | 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 2:07.9040 |
| 24th | 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 2:08.3160 |
| 25th | 7 | Haruhiko Matsumoto / Takayuki Kinoshita | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:08.3990 |
| 26th | 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (ZZW30) | Racing Project Bandoh | 2:08.5790 |
| 27th | 55 | Eiji Yamada / Gou Shimizu | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 2:08.5920 |
| 28th | 910 | Hideshi Matsuda / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 2:08.6710 |
| 29th | 28 | Yukihiro Hane / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Taisan Jr. | 2:08.9180 |
| 30th | 26 | Atsushi Yogou / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan Advan | 2:09.0090 |
| 31st | 24 | Hideo Fukuyama / Mitsuhiro Kinoshita | Porsche 996 GT3-R | Team Taisan Advan | 2:09.0960 |
| 32nd | 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 2:09.2080 |
| 33rd | 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D Sport | 2:09.3400 |
| 34th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 2:09.5500 |
| 35th | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 2:09.5640 |
| 36th | 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 2:09.6810 |
| 37th | 911 | Akira Hirakawa / Shigemitsu Haga | Porsche 996 GT3-RS | 910 Racing | 2:10.3890 |
| 38th | 9 | Masanobu Takenaka / Yousuke Shimojima | Porsche 996 GT3-R | Team Daikokuya | 2:10.4030 |
| 39th | 17 | Masahiro Matsunaga / Takahiro Fujita | Toyota MR-S (ZZW30) | Tom's Spirit | 2:10.8890 |
| 40th | 51 | Naofumi Omoto / Akira Ishikawa | Nissan Silvia (S15) | Auto Staff Racing Team | 2:12.0210 |
| 41st | 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (ZZW30) | KRAFT | 2:12.2400 |
| 42nd | 21 | Yasushi Hitotsuyama / Yasushi Kikuchi | BMW M3 GT (E46) | Hitotsuyama Racing | 2:12.6460 |
| 43rd | 66 | Tetsuya Shimizu / Makoto Shionoiri | Mazda RX-7 (FD3S) | Team Revolution | 2:13.0370 |
| 44th | 70 | Yoshimi Ishibashi / Nobuo Komiya | Porsche 996 GT3-RS | Team Gaikokuya | 2:14.2810 |
| 45th | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (ZZW30) | ARTA With A'pex | 2:15.5770 |
| 46th | 360 | Seigou Nishizawa / Kota Sasaki | Ferrari 360 Modena (GF-F360) | Dentaire Projet Racing | 2:15.9060 |
| 47th | 4 | Naohiro Furuya / Izumi Yoshida | Chevrolet Corvette (C-4) | Zipspeed | 2:22.1970 |