| 1st | 12 | Benoit Tréluyer / Kazuki Hoshino / Jeremie Dufour | Nissan Fairlady Z (Z33) | Team Impul | 1:57.0060 |
| 2nd | 25 | Manabu Orido / Takeshi Tsuchiya / Hideki Noda | Toyota Supra (JZA80) | Toyota Team Tsuchiya | 1:57.2190 |
| 3rd | 8 | Daisuke Ito / Ralph Firman / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Team Honda Racing | 1:57.0440 |
| 4th | 18 | Ryō Michigami / Takashi Kogure / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Team Honda Racing | 1:56.9500 |
| 5th | 6 | Akira Iida / Tatsuya Kataoka / Björn Wirdheim | Lexus SC430 (UZZ40) | Mobil1 Toyota Team Le Mans | 1:57.9530 |
| 6th | 24 | Erik Comas / Masataka Yanagida / Seiji Ara | Nissan Fairlady Z (Z33) | Kondo Racing | 1:58.1580 |
| 7th | 23 | Satoshi Motoyama / Tsugio Matsuda / Yuuji Ide | Nissan Fairlady Z (Z33) | Nismo | 1:58.2310 |
| 8th | 3 | Naoki Yokomizo / Joao Paolo de Oliveira / Darren Manning | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:58.0550 |
| 9th | 100 | Sébastien Philippe / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 1:58.0430 |
| 10th | 22 | Michael Krumm / Fabio Carbone / Richard Lyons | Nissan Fairlady Z (Z33) | Nismo | 1:57.9410 |
| 11th | 66 | André Couto / Katsuyuki Hiranaka / Soheil Ayari | Toyota Supra (JZA80) | Toyota Team Sard | 1:58.2830 |
| 12th | 1 | Yuji Tachikawa / Toranosuke Takagi / Ronnie Quintarelli | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:58.4420 |
| 13th | 36 | Juichi Wakisaka / Andre Lotterer / Adrian Sutil | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:58.6500 |
| 14th | 35 | Naoki Hattori / Peter Dumbreck / Eiichi Tajima | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:58.7720 |
| 15th | 32 | Loïc Duval / Hideki Mutou | Honda NSX (LA-NA2) | Epson Nakajima Racing | 1:57.8380 |
| 17th | 52 | Hironori Takeuchi / Kouki Saga / Keita Sawa | Toyota Celica (ZZT231) | Toyota Team Cerumo | 2:08.7430 |
| 18th | 19 | Kouji Matsuda / Shigekazu Wakisaka | Toyota Celica (ZZT231) | Racing Project Bandoh | 2:08.5110 |
| 19th | 13 | Masami Kageyama / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 2:08.3840 |
| 20th | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui / Akira Watanabe | Vemac RD320R | Team Mach | 2:08.4170 |
| 21st | 47 | Masaoki Nagashima / Hironobu Yasuda | Nissan Fairlady Z (Z33) | Mola | 2:08.5970 |
| 22nd | 62 | Shinsuke Shibahara / Haruki Kurosawa | Vemac RD408R | Willcom R&D Sport | 2:08.8990 |
| 23rd | 7 | Tetsuya Yamano / Hiroyuki Iiri / Shinichi Yamaji | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:09.2430 |
| 24th | 46 | Kota Sasaki / Taku Bamba | Nissan Fairlady Z (Z33) | Mola | 2:09.3200 |
| 25th | 101 | Morio Nitta / Shinichi Takagi | Toyota MR-S (GH-ZZW30) | Apr | 2:08.7650 |
| 26th | 27 | Shogo Mitsuyama / Nobuteru Taniguchi | Vemac RD320R | Direxiv Motorsports | 2:09.0230 |
| 27th | 2 | Kazuho Takahashi / Hiroki Kato / Hiroki Yoshimoto | Shiden MC/RT-16 | Cars Tokai Dream28 | 2:09.5540 |
| 28th | 88 | Marco Apicella / Yasutaka Hinoi / Naohiro Furuya | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 2:09.6610 |
| 29th | 11 | Tetsuya Tanaka / Takayuki Aoki | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:09.7710 |
| 30th | 14 | Mitsuhiro Kinoshita / Kyousuke Mineo / Tomohiko Sunako | Porsche 996 GT3-RS | Endless Sports | 2:09.7720 |
| 31st | 55 | Hidetoshi Mitsusada / Daisuke Ikeda / Hiroaki Ishiura | Ford GT (DHG-replica) | Dhg Racing | 2:10.0790 |
| 32nd | 10 | Hiromi Kozono / Naofumi Omoto / Eiji Yamada | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:10.1010 |
| 33rd | 87 | Koji Yamanishi / Hisashi Wada / Atsushi Yogo | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 2:10.1080 |
| 34th | 910 | Tadao Uematsu / Yasushi Kikuchi / Ryohei Sakaguchi | Porsche 996 GT3-RSR | 910 Racing With Team Ishimatsu | 2:10.4380 |
| 35th | 110 | Hideshi Matsuda / Ichijou Suga / Takaya Tsubobayashi | Porsche 986 Boxster | Arktech Motorsports | 2:10.5300 |
| 36th | 9 | Osamu Nakajima / Masaki Tanaka / Akira Yoshimoto | Mosler MT900R | A&S Racing | 2:10.7620 |
| 37th | 96 | Takuya Kurosawa / Tsubasa Kurosawa | Vemac RD350R | Ebbro Team Nova | 2:11.1150 |
| 38th | 70 | Yoshimi Ishibashi / Isao Ihashi / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Gaikokuya | 2:12.1110 |
| 39th | 111 | Hiroya Iijima / Masaki Jounai / Takeshi Namekawa | Porsche 996 GT3 Cup | Team LeyJun | 2:15.6480 |
| 40th | 777 | Minoru Tanaka / Kazuya Oshima / Keiichi Kobayashi | Toyota MR-S (GH-ZZW30) | Ryouzanpaku With Apr | 2:11.4310 |