| 1st | 1 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:45.8550 |
| 2nd | 38 | Yuuji Tachikawa / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:46.0050 |
| 3rd | 22 | Michael Krumm / Tsugio Matsuda | Nissan Fairlady Z (Z33) | Nismo | 1:46.0670 |
| 4th | 100 | Shin'ya Hosokawa / Dominik Schwager | Honda NSX (LA-NA2) | Team Kunimitsu | 1:46.1360 |
| 5th | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Dome Racing Team | 1:46.2630 |
| 6th | 3 | Sébastien Philippe / Masataka Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:46.3370 |
| 7th | 25 | Takeshi Tsuchiya / Manabu Orido | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:46.3380 |
| 8th | 23 | Satoshi Motoyama / Hironobu Yasuda / Richard Lyons | Nissan Fairlady Z (Z33) | Nismo | 1:46.3860 |
| 9th | 32 | Loic Duval / Fabio Carbone | Honda NSX (LA-NA2) | Nakajima Racing | 1:46.3930 |
| 10th | 12 | Kazuki Hoshino / Jeremie Dufour | Nissan Fairlady Z (Z33) | Team Impul | 1:46.4160 |
| 11th | 8 | Daisuke Itou / Ralph Firman / Yuuji Ide | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:46.5160 |
| 12th | 6 | Tatsuya Kataoka / Björn Wirdheim | Lexus SC430 (UZZ40) | Forum Eng. Toyota Team Le Mans | 1:46.5310 |
| 13th | 17 | Katsutomo Kaneishi / Toshihiro Kaneishi / Takuya Izawa | Honda NSX (LA-NA2) | Rolling Stone Real Racing | 1:46.5570 |
| 14th | 39 | André Couto / Katsuyuki Hiranaka | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:46.8180 |
| 15th | 35 | Naoki Hattori / Ronnie Quintarelli | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:46.9480 |
| 16th | 350 | | Nissan Fairlady Z (Z33) | Nismo | 1:47.0410 |
| 17th | 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan Fairlady Z (Z33) | Kondo Racing | 1:47.2490 |
| 18th | 62 | Shinsuke Shibahara / Haruki Kurosawa | Vemac RD408R | Willcom R&D Sport | 1:56.1100 |
| 19th | 2 | Kazuho Takahashi / Hiroki Katou / Hiroki Yoshimoto | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:56.2350 |
| 20th | 46 | Kota Sasaki / Naoki Yokomizo | Nissan Fairlady Z (Z33) | Mola | 1:56.2750 |
| 21st | 13 | Masami Kageyama / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 1:56.4040 |
| 22nd | 666 | Syougo Suhou / Jun'ichirou Yamashita / Masato Shimoyama | Vemac RD320R | Avanzza x Bomex | 1:56.4290 |
| 23rd | 110 | Takuya Kurosawa / Hidetoshi Mitsusada | Porsche 986 Boxster | Arktech Motorsports | 1:56.5270 |
| 24th | 55 | Daisuke Ikeda / Taku Bamba | Ford GT (DHG-replica) | Dhg Racing | 1:56.6200 |
| 25th | 111 | Yasushi Kikuchi / Takeshi Namekawa / Masaki Jounai | Porsche 986 Boxster | Arktech Motorsports | 1:56.7470 |
| 26th | 33 | Mitsuhiro Kinoshita / Yuuya Sakamoto | Porsche 996 GT3-R | Hankook Ktr | 1:56.7480 |
| 27th | 11 | Masayuki Ueda / Ichijou Suga / Hideshi Matsuda | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:57.1010 |
| 28th | 47 | Shigekazu Wakisaka / Shogo Mitsuyama | Nissan Fairlady Z (Z33) | Mola | 1:57.1190 |
| 29th | 77 | Tetsuya Yamano / Takayuki Aoki / Katsuo Kobayashi | Subaru Impreza (GD) | Cusco Racing | 1:58.1000 |
| 30th | 19 | Akira Iida / Yuuhi Sekiguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:58.3520 |