| 1st | 3 | Sébastien Philippe / Masataka Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:56.2000 |
| 2nd | 32 | Loïc Duval / Fabio Carbone | Honda NSX (LA-NA2) | Nakajima Racing | 1:55.8170 |
| 3rd | 25 | Takeshi Tsuchiya / Manabu Orido | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:56.2640 |
| 4th | 38 | Yuuji Tachikawa / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:56.5120 |
| 5th | 8 | Daisuke Itou / Ralph Firman / Yuuji Ide | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:56.2840 |
| 6th | 100 | Shin'ya Hosokawa / Dominik Schwager | Honda NSX (LA-NA2) | Team Kunimitsu | 1:56.4050 |
| 7th | 17 | Katsutomo Kaneishi / Toshihiro Kaneishi / Takuya Izawa | Honda NSX (LA-NA2) | Rolling Stone Real Racing | 1:56.2940 |
| 8th | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Dome Racing Team | 1:56.1410 |
| 9th | 6 | Tatsuya Kataoka / Björn Wirdheim | Lexus SC430 (UZZ40) | Forum Eng. Toyota Team Le Mans | 1:56.3790 |
| 10th | 12 | Benoit Tréluyer / Kazuki Hoshino / Jeremie Dufour | Nissan Fairlady Z (Z33) | Team Impul | 1:55.9810 |
| 11th | 1 | Juichi Wakisaka / Oliver Jarvis / Andre Lotterer | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:56.8670 |
| 12th | 35 | Naoki Hattori / Peter Dumbreck / Ronnie Quintarelli | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:56.8960 |
| 13th | 23 | Satoshi Motoyama / Hironobu Yasuda / Richard Lyons | Nissan Fairlady Z (Z33) | Nismo | 1:56.9100 |
| 14th | 22 | Michael Krumm / Tsugio Matsuda | Nissan Fairlady Z (Z33) | Nismo | 1:57.0840 |
| 15th | 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan Fairlady Z (Z33) | Kondo Racing | 1:57.5650 |
| 16th | 39 | André Couto / Katsuyuki Hiranaka | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:57.9030 |
| 17th | 2 | Kazuho Takahashi / Hiroki Katou / Hiroki Yoshimoto | Shiden MC/RT-16 | Cars Tokai Dream28 | 2:07.1540 |
| 18th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 2:06.6960 |
| 19th | 62 | Shinsuke Shibahara / Haruki Kurosawa | Vemac RD408R | Willcom R&D Sport | 2:07.0050 |
| 20th | 13 | Masami Kageyama / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 2:07.0210 |
| 21st | 26 | Nobuteru Taniguchi / Dominik Farnbacher / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 2:07.5970 |
| 22nd | 31 | Kyousuke Mineo / Yuuya Sakamoto | Toyota MR-S (GH-ZZW30) | Apr | 2:07.3320 |
| 23rd | 101 | Kazuya Oshima / Hiroaki Ishiura | Toyota MR-S (GH-ZZW30) | Apr | 2:07.1800 |
| 24th | 7 | Hiroyuki Iiri / Ryou Orime / Naoya Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:07.7220 |
| 25th | 5 | Tetsuji Tamanaka / Hironori Takeuchi / Keita Sawa | Vemac RD320R | Team Mach | 2:07.6740 |
| 26th | 77 | Tetsuya Yamano / Takayuki Aoki / Katsuo Kobayashi | Subaru Impreza (GD) | Cusco Racing | 2:07.3300 |
| 27th | 46 | Kota Sasaki / Naoki Yokomizo | Nissan Fairlady Z (Z33) | Mola | 2:07.7910 |
| 28th | 4 | Tetsuya Tanaka / Shinsuke Yamazaki / Akira Watanabe | Vemac RD350R | Ebbro Team Nova | 2:07.8880 |
| 29th | 55 | Daisuke Ikeda / Taku Bamba / Hideo Fukuyama | Ford GT (DHG-replica) | Dhg Racing | 2:07.9030 |
| 30th | 11 | Masayuki Ueda / Ichijou Suga / Hideshi Matsuda | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:08.5580 |
| 31st | 19 | Akira Iida / Yuuhi Sekiguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 2:08.7640 |
| 32nd | 110 | Takuya Kurosawa / Hidetoshi Mitsusada | Porsche 986 Boxster | Arktech Motorsports | 2:08.7700 |
| 33rd | 47 | Shigekazu Wakisaka / Shogo Mitsuyama | Nissan Fairlady Z (Z33) | Mola | 2:08.8110 |
| 34th | 33 | Mitsuhiro Kinoshita / Yuuya Sakamoto | Porsche 996 GT3-R | Hankook Ktr | 2:09.2580 |
| 35th | 333 | Tadao Uematsu / Ryohei Sakaguchi / Takashi Inoue | Porsche 996 GT3-RSR | Mario Racing With Ishimatsu | 2:09.3740 |
| 36th | 111 | Yasushi Kikuchi / Masaki Jounai / Takaya Tsubobayashi | Porsche 986 Boxster | Arktech Motorsports | 2:09.3750 |
| 37th | 666 | Syougo Suhou / Jun'ichirou Yamashita / Masato Shimoyama | Vemac RD320R | Avanzza x Bomex | 2:09.4580 |
| 38th | 9 | Masaki Tanaka / Katsuhiko Tsutsui / Osamu Nakajima | Mosler MT900R (OOX) | A&S Racing | 2:10.2370 |
| 39th | 70 | Yoshimi Ishibashi / Hiroshi Koizumi / "Akazame Oyaji" | Porsche 996 GT3-RS | Team Gaikokuya | 2:12.5790 |
| 40th | 67 | Tsubasa Kurosawa / Hisashi Wada / Naohiro Furuya | Lamborghini Gallardo RG-3 | JLOC | 2:15.8810 |