| 1st | 36 | Takeshi Tsuchiya / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:59.8000 |
| 2nd | 64 | Ralph Firman / Tsugio Matsuda | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:59.8040 |
| 3rd | 18 | Sébastien Philippe / Richard Lyons | Honda NSX (LA-NA2) | Dome Mugen Project | 2:00.0040 |
| 4th | 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 2:00.2320 |
| 5th | 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 2:00.2360 |
| 6th | 16 | Dominik Schwager / Daisuke Itou | Honda NSX (LA-NA2) | Dome Mugen Project | 2:00.2480 |
| 7th | 23 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 2:00.2540 |
| 8th | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 2:00.3500 |
| 10th | 22 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 2:00.5960 |
| 11th | 12 | Tetsuya Tanaka / Kazuyoshi Hoshino | Nissan Skyline GT-R (BNR34) | Team Impul | 2:00.6050 |
| 12th | 37 | Takuya Kurosawa / Paolo Montin | Toyota Supra (JZA80) | Toyota Team Tom's | 2:00.6840 |
| 13th | 25 | Shin'ichi Yamaji / Seiji Ara | Toyota Supra (JZA80) | Tsuchiya Engineering | 2:00.8690 |
| 14th | 76 | Naoki Hattori / Eiichi Tajima | McLaren F1 GTR (19R GTR) | Hitotsuyama Racing | 2:01.6370 |
| 15th | 33 | Masahiko Kondou / Hayanari Shimoda | Toyota Supra (JZA80) | Toyota Team Cerumo | 2:02.3990 |
| 16th | 39 | Jeremie Dufour / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 2:02.4030 |
| 17th | 35 | Masahiko Kageyama / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 2:03.1030 |
| 18th | 88 | Marco Apicella / Hisashi Wada | Lamborghini Diablo JGT-1 (ZA90DE068) | JLOC | 2:06.6660 |
| 19th | 3 | Tetsuya Yamano / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 2:10.4520 |
| 20th | 7 | Haruhiko Matsumoto / Nobuteru Taniguchi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:10.5420 |
| 21st | 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 2:10.7340 |
| 22nd | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (ZZW30) | ARTA With A'pex | 2:10.9660 |
| 23rd | 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (ZZW30) | Racing Project Bandoh | 2:11.1350 |
| 24th | 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 2:11.3030 |
| 25th | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 2:11.5750 |
| 26th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 2:11.5980 |
| 27th | 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (ZZW30) | KRAFT | 2:11.9270 |
| 28th | 24 | Hideo Fukuyama / Mitsuhiro Kinoshita | Porsche 996 GT3-R | Team Taisan Advan | 2:11.9950 |
| 29th | 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 2:12.4280 |
| 30th | 55 | Eiji Yamada / Takayuki Kinoshita | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 2:12.4820 |
| 31st | 26 | Atsushi Yogou / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan Advan | 2:12.7840 |
| 32nd | 910 | Hideshi Matsuda / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 2:12.8630 |
| 33rd | 28 | Yukihiro Hane / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Taisan Jr. | 2:13.0380 |
| 34th | 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 2:13.6800 |
| 35th | 9 | Yousuke Shimojima / Masanobu Takenaka | Porsche 996 GT3-R | Team Daikokuya | 2:13.7320 |
| 36th | 61 | Yasuo Miyagawa / Atsushi Katsumata | Porsche 996 GT3-RS | R&D Sport Ex | 2:14.9750 |
| 37th | 70 | Yoshimi Ishibashi / Patrick van Schoote | Porsche 996 GT3-RS | Team Gaikokuya | 2:16.3640 |
| 38th | 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D Sport | 2:16.7530 |
| 39th | 21 | Yasushi Hitotsuyama / Yasushi Kikuchi | BMW M3 GT (E46) | Hitotsuyama Racing | 2:16.8690 |