| 1st | 32 | Andre Lotterer / Tsugio Matsuda | Honda NSX (LA-NA2) | Nakajima Racing | 1:35.3630 |
| 2nd | 36 | Takeshi Tsuchiya / James Courtney | Toyota Supra (JZA80) | Toyota Team Tom's | 1:35.1590 |
| 3rd | 37 | Tatsuya Kataoka / Sakon Yamamoto | Toyota Supra (JZA80) | Toyota Team Tom's | 1:35.5920 |
| 4th | 38 | Toranosuke Takagi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:35.0120 |
| 5th | 8 | Ralph Firman / Daisuke Itou | Honda NSX (LA-NA2) | Team Honda Racing | 1:35.1750 |
| 6th | 6 | Akira Iida / Juichi Wakisaka | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:35.2300 |
| 7th | 39 | André Couto / Ronnie Quintarelli | Toyota Supra (JZA80) | Toyota Team SARD | 1:35.6310 |
| 8th | 3 | Toshihiro Kaneishi / Erik Comas | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:35.2220 |
| 9th | 25 | Manabu Orido / Hideki Noda | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:35.6580 |
| 10th | 22 | Masataka Yanagida / Michael Krumm | Nissan Fairlady Z (Z33) | NISMO | 1:35.8900 |
| 11th | 1 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | NISMO | 1:35.9160 |
| 12th | 12 | Benoit Tréluyer / Yuuji Ide | Nissan Fairlady Z (Z33) | Team Impul | 1:35.9600 |
| 13th | 34 | Naoki Yokomizo / Seiji Ara | Toyota Supra (JZA80) | KRAFT | 1:35.9610 |
| 14th | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Honda Racing | 1:36.5120 |
| 15th | 100 | Sébastien Philippe / Jeremie Dufour | Honda NSX (LA-NA2) | Team Kunimitsu | 1:36.5280 |
| 16th | 21 | Takuya Kurosawa / Hidetoshi Mitsusada | Ferrari 550 Maranello GTS | Hitotsuyama Racing | 1:36.6150 |
| 17th | 20 | Mikio Hitotsuyama / Eiichi Tajima | McLaren F1 GTR (4S70) | Hitotsuyama Racing | 1:37.4050 |
| 18th | 88 | Kouji Yamanishi / Naohiro Furuya | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:40.3900 |
| 19th | 35 | Peter Dumbreck / Naoki Hattori | Toyota Supra (JZA80) | KRAFT | 1:47.6530 |
| 21st | 0 | Haruki Kurosawa / Shin'ya Hosokawa | Honda NSX (LA-NA2) | M-Tec Co.Ltd. | 1:42.8610 |
| 22nd | 10 | Yasutaka Hinoi / Taku Bamba | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:43.4460 |
| 23rd | 13 | Masami Kageyama / Mitsuhiro Kinoshita | Nissan Fairlady Z (Z33) | Endless Sports | 1:43.3000 |
| 24th | 11 | Tetsuya Tanaka / Paolo Montin | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:43.4880 |
| 25th | 46 | Kazuki Hoshino / Takayuki Aoki | Nissan Fairlady Z (Z33) | Mola | 1:42.8300 |
| 26th | 30 | Kota Sasaki / Tetsuya Yamano | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:43.8650 |
| 27th | 62 | Shinsuke Shibahara / Tadao Uematsu | Vemac RD350R | Willcom R&D Sport | 1:42.9720 |
| 28th | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 1:43.2150 |
| 29th | 2 | Kazuho Takahashi / Akira Watanabe | Vemac RD320R | Verno Tokai Dream28 | 1:43.3950 |
| 30th | 7 | Shin'ichi Yamaji / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:43.4510 |
| 31st | 27 | Yasuo Miyagawa / Shogo Mitsuyama | Vemac RD320R | Direxiv Motorsports | 1:43.9440 |
| 32nd | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (SA9VGR) | Autobacs Racing Team Aguri | 1:43.9630 |
| 33rd | 9 | Eiji Yamada / Jun'ichirou Yamashita | Mosler MT900R | A&S Racing | 1:44.0930 |
| 34th | 31 | Minoru Tanaka / Kazuki Nakajima | Toyota MR-S (GH-ZZW30) | Kicchouhouzan With Apr | 1:44.1130 |
| 35th | 19 | Nobuteru Taniguchi / Hiroki Katou | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:44.1980 |
| 36th | 47 | Gou Shimizu / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Mola | 1:44.2920 |
| 37th | 52 | Hironori Takeuchi / Katsuyuki Hiranaka | Toyota Celica (ZZT231) | Toyota Team Cerumo | 1:44.4050 |
| 38th | 87 | Marco Apicella / Hisashi Wada | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:44.5970 |
| 39th | 777 | Tomohiko Sunako / Kazuyoshi Takamizawa | Porsche 996 GT3-RS | 910 Racing | 1:45.2420 |
| 40th | 111 | Hiroya Iijima / Masaki Jounai | Porsche 968 (E-968) | Team LeyJun | 1:45.7500 |
| 41st | 72 | Hiroshi Wada / Akira Hirakawa | Porsche 996 GT3-RSR | Teramoto Technical Office | 1:46.4510 |
| 42nd | 70 | Yoshimi Ishibashi / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Gaikokuya | 1:46.5440 |
| 43rd | 110 | Takashi Ooi / Ichijou Suga | Porsche 986 Boxster | Arktech Motorsports | 1:46.6850 |
| 44th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 1:48.0820 |
| 45th | 913 | Syougo Suhou / Hideo Fukuyama | Chevrolet Corvette C6 (GH-X245) | A&S Racing | 1:49.7020 |
| 46th | 112 | Atsushi Yogou / Takaya Tsubobayashi | Porsche 996 GT3 (GF99663) | Arktech Motorsports | |