| 1st | 36 | Takeshi Tsuchiya / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:46.8580 |
| 2nd | 18 | Sébastien Philippe / Richard Lyons | Honda NSX (LA-NA2) | Dome Mugen Project | 1:46.9310 |
| 3rd | 30 | Hideki Okada / Haruki Kurosawa | McLaren F1 GTR (19R GTR) | Team Take One | 1:47.0290 |
| 4th | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:47.0630 |
| 5th | 39 | Jeremie Dufour / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:47.3620 |
| 6th | 23 | Masami Kageyama / Erik Comas | Nissan Skyline GT-R (BNR34) | NISMO | 1:47.4230 |
| 7th | 16 | Ryou Michigami / Daisuke Itou | Honda NSX (LA-NA2) | Dome Mugen Project | 1:47.4420 |
| 8th | 76 | Naoki Hattori / Eiichi Tajima | McLaren F1 GTR (19R GTR) | Hitotsuyama Racing | 1:47.4770 |
| 9th | 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:47.6590 |
| 10th | 12 | Tetsuya Tanaka / Benoit Tréluyer | Nissan Skyline GT-R (BNR34) | Team Impul | 1:47.7730 |
| 11th | 64 | Tsugio Matsuda / Ralph Firman | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:47.8460 |
| 12th | 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:47.8720 |
| 13th | 35 | Masahiko Kageyama / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:48.1210 |
| 14th | 37 | Takuya Kurosawa / Paolo Montin | Toyota Supra (JZA80) | Toyota Team Tom's | 1:48.1260 |
| 15th | 25 | Seiji Ara / Shin'ichi Yamaji | Toyota Supra (JZA80) | Tsuchiya Engineering | 1:48.1440 |
| 16th | 1 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:48.3080 |
| 17th | 22 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:48.3180 |
| 18th | 33 | Masahiko Kondou / Hayanari Shimoda | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:48.8280 |
| 19th | 88 | Marco Apicella / Hisashi Wada | Lamborghini Diablo JGT-1 (ZA90DE068) | JLOC | 1:50.9680 |
| 20th | 87 | Kouji Yamanishi / Yuudai Igarashi | Mercedes-Benz CLK (GF-208) | HKS | 1:55.7260 |
| 21st | 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 1:56.8820 |
| 22nd | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 1:57.5090 |
| 23rd | 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (ZZW30) | ARTA With A'pex | 1:57.6200 |
| 24th | 24 | Hideo Fukuyama / Mitsuhiro Kinoshita | Porsche 996 GT3-R | Team Taisan Advan | 1:57.6660 |
| 25th | 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (ZZW30) | KRAFT | 1:57.7450 |
| 26th | 3 | Tetsuya Yamano / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 1:57.8870 |
| 27th | 26 | Atsushi Yogou / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan Advan | 1:57.9870 |
| 28th | 28 | Yukihiro Hane / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Taisan Jr. | 1:58.2460 |
| 29th | 7 | Haruhiko Matsumoto / Nobuteru Taniguchi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:58.2810 |
| 30th | 55 | Eiji Yamada / Gou Shimizu | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 1:58.3590 |
| 31st | 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 1:58.3830 |
| 32nd | 910 | Hideshi Matsuda / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 1:58.4460 |
| 33rd | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:58.4650 |
| 34th | 71 | Masaki Jounai / Keita Sawa | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 1:58.5830 |
| 35th | 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (ZZW30) | Racing Project Bandoh | 1:59.3280 |
| 36th | 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:59.8800 |
| 37th | 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 1:59.9020 |
| 38th | 911 | Akira Hirakawa / Shigemitsu Haga | Porsche 996 GT3-RS | 910 Racing | 1:59.9150 |
| 39th | 21 | Mikio Hitotsuyama / Yasushi Kikuchi | BMW M3 GT (E46) | Hitotsuyama Racing | 2:00.4450 |
| 40th | 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D Sport | 2:00.5500 |
| 41st | 66 | Tetsuya Shimizu / Makoto Shionoiri | Mazda RX-7 (FD3S) | Team Revolution | 2:03.3010 |
| 42nd | 70 | Yoshimi Ishibashi / Seiichi Sodeyama | Porsche 996 GT3-RS | Team Gaikokuya | 2:03.9500 |
| 43rd | 4 | Naohiro Furuya / Izumi Yoshida | Chevrolet Corvette (C-4) | Zipspeed | 2:07.9950 |