| 1st | 8 | Daisuke Itou / Ralph Firman | Honda NSX (LA-NA2) | Team Honda Racing | 1:58.6420 |
| 2nd | 22 | Michael Krumm / Richard Lyons | Nissan Fairlady Z (Z33) | Nismo | 1:58.9900 |
| 3rd | 1 | Yuuji Tachikawa / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:59.5540 |
| 4th | 12 | Benoit Tréluyer / Kazuki Hoshino | Nissan Fairlady Z (Z33) | Team Impul | 1:58.8490 |
| 5th | 36 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:59.6770 |
| 6th | 100 | Sébastien Philippe / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 2:00.2470 |
| 7th | 3 | Naoki Yokomizo / Joao Paolo de Oliveira | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:59.9420 |
| 8th | 23 | Satoshi Motoyama / Tsugio Matsuda | Nissan Fairlady Z (Z33) | Nismo | 2:00.1320 |
| 9th | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Honda Racing | 1:59.7810 |
| 10th | 24 | Erik Comas / Masataka Yanagida | Nissan Fairlady Z (Z33) | Kondo Racing | 2:00.4300 |
| 11th | 32 | Loic Duval / Hideki Mutou | Honda NSX (LA-NA2) | Epson Nakajima Racing | 2:00.4630 |
| 12th | 6 | Akira Iida / Tatsuya Kataoka | Lexus SC430 (UZZ40) | Mobil1 Toyota Team Le Mans | 2:00.5090 |
| 13th | 25 | Manabu Orido / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Team Tsuchiya | 2:00.7730 |
| 14th | 66 | André Couto / Katsuyuki Hiranaka | Toyota Supra (JZA80) | Toyota Team Sard | 2:01.2860 |
| 15th | 35 | Naoki Hattori / Peter Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 2:01.8020 |
| 17th | 2 | Kazuho Takahashi / Hiroki Katou | Shiden MC/RT-16 | Verno Tokai Dream28 | 2:09.9650 |
| 18th | 13 | Masami Kageyama / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 2:10.5660 |
| 19th | 7 | Tetsuya Yamano / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:09.6740 |
| 20th | 19 | Kouji Matsuda / Shigekazu Wakisaka | Toyota Celica (ZZT231) | Racing Project Bandoh | 2:10.0360 |
| 21st | 55 | Hidetoshi Mitsusada / Daisuke Ikeda | Ford GT (DHG-replica) | Dhg Racing | 2:10.3690 |
| 22nd | 110 | Hideshi Matsuda / Ichijou Suga | Porsche 986 Boxster | Arktech Motorsports | 2:10.6880 |
| 23rd | 14 | Mitsuhiro Kinoshita / Kyousuke Mineo | Porsche 996 GT3-RS | Endless Sports | 2:10.6090 |
| 24th | 96 | Takuya Kurosawa / Tsubasa Kurosawa | Vemac RD350R | Ebbro Team Nova | 2:10.1130 |
| 25th | 11 | Tetsuya Tanaka / Takayuki Aoki | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:10.7130 |
| 26th | 27 | Shogo Mitsuyama / Nobuteru Taniguchi | Vemac RD320R | Direxiv Motorsports | 2:10.3940 |
| 27th | 62 | Shinsuke Shibahara / Hiroyuki Yagi | Vemac RD408R | Willcom R&D Sport | 2:10.7630 |
| 28th | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 2:10.8210 |
| 29th | 101 | Morio Nitta / Shinichi Takagi | Toyota MR-S (GH-ZZW30) | Apr | 2:10.9060 |
| 30th | 47 | Masaoki Nagashima / Hironobu Yasuda | Nissan Fairlady Z (Z33) | Mola | 2:11.0260 |
| 31st | 46 | Kota Sasaki / Taku Bamba | Nissan Fairlady Z (Z33) | Mola | 2:11.2930 |
| 32nd | 777 | Minoru Tanaka / Kazuya Oshima | Toyota MR-S (GH-ZZW30) | Ryouzanpaku With Apr | 2:11.5630 |
| 33rd | 10 | Hiromi Kozono / Naofumi Omoto | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:11.9850 |
| 34th | 910 | Tadao Uematsu / Yasushi Kikuchi | Porsche 996 GT3-RSR | 910 Racing With Team Ishimatsu | 2:12.1210 |
| 35th | 70 | Yoshimi Ishibashi / Akira Hirakawa | Porsche 996 GT3-RS | Team Gaikokuya | 2:13.9950 |
| 36th | 666 | Syougo Suhou / Jun'ichirou Yamashita | Honda NSX (GH-NA2) | Team Bomex Dream28 | 2:14.1710 |