| 1st | 38 | Yuuji Tachikawa / Toranosuke Takagi | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:34.9640 |
| 2nd | 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:33.9020 |
| 3rd | 22 | Michael Krumm / Masataka Yanagida | Nissan Fairlady Z (Z33) | NISMO | 1:34.6700 |
| 4th | 8 | Ralph Firman / Daisuke Itou | Honda NSX (LA-NA2) | Team Honda Racing | 1:34.6960 |
| 5th | 37 | Tatsuya Kataoka / Sakon Yamamoto | Toyota Supra (JZA80) | Toyota Team Tom's | 1:34.1470 |
| 6th | 36 | Takeshi Tsuchiya / James Courtney | Toyota Supra (JZA80) | Toyota Team Tom's | 1:34.4680 |
| 7th | 35 | Shigekazu Wakisaka / Naoki Hattori | Toyota Supra (JZA80) | KRAFT | 1:34.1410 |
| 8th | 12 | Yuuji Ide / Benoit Tréluyer | Nissan Fairlady Z (Z33) | Team Impul | 1:34.2730 |
| 9th | 32 | Andre Lotterer / Tsugio Matsuda | Honda NSX (LA-NA2) | Nakajima Racing | 1:35.0140 |
| 10th | 39 | André Couto / Ronnie Quintarelli | Toyota Supra (JZA80) | Toyota Team SARD | 1:34.7980 |
| 11th | 1 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | NISMO | 1:35.0010 |
| 12th | 34 | Seiji Ara / Naoki Yokomizo | Toyota Supra (JZA80) | KRAFT | 1:34.4450 |
| 13th | 3 | Erik Comas / Toshihiro Kaneishi | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:35.2620 |
| 14th | 25 | Dominik Schwager / Manabu Orido | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:35.3250 |
| 15th | 100 | Sébastien Philippe / Jeremie Dufour | Honda NSX (LA-NA2) | Team Kunimitsu | 1:35.5330 |
| 16th | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Honda Racing | 1:35.6050 |
| 17th | 20 | Eiichi Tajima / Yasushi Hitotsuyama | McLaren F1 GTR (4S70) | Hitotsuyama Racing | 1:36.1660 |
| 18th | 21 | Hidetoshi Mitsusada / Takuya Kurosawa | Ferrari 550 Maranello GTS | Hitotsuyama Racing | 1:37.3700 |
| 19th | 88 | Kouji Yamanishi / Hisashi Wada | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:39.6350 |
| 21st | 0 | Haruki Kurosawa / Shin'ya Hosokawa | Honda NSX (LA-NA2) | M-Tec Co.Ltd. | 1:41.1590 |
| 22nd | 46 | Kazuki Hoshino / Takayuki Aoki | Nissan Fairlady Z (Z33) | Mola | 1:41.8600 |
| 23rd | 27 | Shogo Mitsuyama / Yasuo Miyagawa | Vemac RD320R | Direxiv Motorsports | 1:41.2650 |
| 24th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (SA9VGR) | Autobacs Racing Team Aguri | 1:41.9000 |
| 25th | 10 | Yasutaka Hinoi / Taku Bamba | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:41.7310 |
| 26th | 30 | Kota Sasaki / Tetsuya Yamano | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:42.2800 |
| 27th | 62 | Tadao Uematsu / Shinsuke Shibahara | Vemac RD350R | Willcom R&D Sport | 1:42.3100 |
| 28th | 11 | Tetsuya Tanaka / Paolo Montin | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:41.8970 |
| 29th | 31 | Minoru Tanaka / Kazuki Nakajima | Toyota MR-S (GH-ZZW30) | Apexera With Apr | 1:42.2370 |
| 30th | 7 | Shin'ichi Yamaji / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:41.8430 |
| 31st | 52 | Katsuyuki Hiranaka / Hironori Takeuchi | Toyota Celica (ZZT231) | Toyota Team Cerumo | 1:42.3920 |
| 32nd | 2 | Akira Watanabe / Kazuho Takahashi | Vemac RD320R | Verno Tokai Dream28 | 1:42.4800 |
| 33rd | 47 | Tomonobu Fujii / Gou Shimizu | Nissan Fairlady Z (Z33) | Mola | 1:42.6450 |
| 34th | 77 | Tatsuya Tanigawa / Katsuo Kobayashi | Subaru Impreza (GDB) | Cusco Racing | 1:42.6790 |
| 35th | 13 | Masami Kageyama / Mitsuhiro Kinoshita | Nissan Fairlady Z (Z33) | Endless Sports | 1:43.0740 |
| 36th | 19 | Nobuteru Taniguchi / Hiroki Katou | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:43.2770 |
| 37th | 777 | Kazuyoshi Takamizawa / Tomohiko Sunako | Porsche 996 GT3-RS | 910 Racing | 1:43.6420 |
| 38th | 9 | Eiji Yamada / Jun'ichirou Yamashita | Mosler MT900R | A&S Racing | 1:43.8580 |
| 39th | 26 | Yutaka Yamagishi / Kaoru Ijiri | Porsche 996 GT3-RS | Team Taisan Advan | 1:43.9980 |
| 40th | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 1:44.7810 |
| 41st | 112 | Keita Sawa / Atsushi Yogou | Porsche 996 GT3 (GF99663) | Arktech Motorsports | 1:44.9090 |
| 42nd | 72 | Hiroshi Wada / Akira Hirakawa | Porsche 996 GT3-RSR | Teramoto Technical Office | 1:45.1250 |
| 43rd | 111 | Masaki Jounai / Hiroya Iijima | Porsche 968 (E-968) | Team LeyJun | 1:47.2380 |
| 44th | 70 | Yoshimi Ishibashi / Hiroshi Takei | Porsche 996 GT3-RS | Team Gaikokuya | 1:48.0730 |
| 45th | 913 | Hideo Fukuyama / Syougo Suhou | Chevrolet Corvette C6 | A&S Racing | 1:48.4530 |
| 46th | 110 | Ichijou Suga / Takashi Ooi | Porsche 986 Boxster | Arktech Motorsports | 1:51.5760 |