| 1st | 18 | Takashi Kogure / Ryou Michigami | Honda NSX (LA-NA2) | Dome Racing Team | 1:41.8840 |
| 2nd | 38 | Yuuji Tachikawa / Richard Lyons | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:42.0950 |
| 3rd | 35 | Peter Dumbreck / Tatsuya Kataoka | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:42.0740 |
| 4th | 17 | Toshihiro Kaneishi / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Real Racing With Leon | 1:42.6680 |
| 5th | 36 | Andre Lotterer / Juichi Wakisaka | Lexus SC430 (UZZ40) | Petronas Toyota Team Tom's | 1:42.1750 |
| 6th | 100 | Yuuji Ide / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 1:42.4900 |
| 7th | 32 | Loic Duval / Katsuyuki Hiranaka | Honda NSX (LA-NA2) | Nakajima Racing | 1:41.1150 |
| 8th | 39 | André Couto / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:40.9850 |
| 9th | 25 | Takeshi Tsuchiya / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:42.2450 |
| 10th | 12 | Sébastien Philippe / Tsugio Matsuda | Nissan GT-R | Team Impul | 1:42.5060 |
| 11th | 1 | Ralph Firman / Takuya Izawa | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:43.1810 |
| 12th | 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan GT-R | Kondo Racing | 1:43.2160 |
| 13th | 23 | Benoit Tréluyer / Satoshi Motoyama | Nissan GT-R | Nismo | 1:43.4630 |
| 14th | 3 | Ronnie Quintarelli / Naoki Yokomizo | Nissan GT-R | Hasemi Motorsport | 1:43.4990 |
| 15th | 22 | Michael Krumm / Masataka Yanagida | Nissan GT-R | Nismo | 1:43.7770 |
| 16th | 6 | Daisuke Itou / Björn Wirdheim | Lexus SC430 (UZZ40) | Eneos Toyota Team Le Mans | no time |
| 17th | 95 | Kouhei Hirate / Keisuke Kunimoto | Toyota MR-S (GH-ZZW30) | Apr | 1:53.3260 |
| 18th | 110 | Hidetoshi Mitsusada / Daisuke Ikeda | Porsche 986 Boxster | Arktech Motorsports | 1:53.4920 |
| 19th | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:53.6580 |
| 20th | 77 | Kota Sasaki / Tetsuya Yamano | Subaru Impreza (GD) | Cusco Racing | 1:50.4810 |
| 21st | 33 | Masami Kageyama / Mitsuhiro Kinoshita | Porsche 997 GT3 RSR | Hankook KTR | 1:53.1320 |
| 22nd | 7 | Hiroyuki Iiri / Ryou Orime | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:53.8580 |
| 23rd | 19 | Manabu Orido / Tsubasa Abe | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:50.5560 |
| 24th | 4 | Ryohei Sakaguchi / Masaki Matsushita | Vemac RD320R | Team Uematsu Nova | 1:53.4690 |
| 25th | 5 | Tetsuji Tamanaka / Naoya Yamano | Vemac RD320R | Team Mach | 1:52.8020 |
| 26th | 88 | Naohiro Furuya / Hideshi Matsuda | Lamborghini Gallardo RG-3 | JLOC | 1:53.2360 |
| 27th | 46 | Kazuki Hoshino / Hironobu Yasuda | Nissan Fairlady Z (Z33) | Mola | 1:54.0520 |
| 28th | 31 | Yuuya Sakamoto / Kyousuke Mineo | Toyota MR-S (GH-ZZW30) | Apr | 1:54.3340 |
| 29th | 70 | Yutaka Yamagishi / "Akazame Oyaji" | Porsche 996 GT3-RS | Team Gaikokuya | 1:54.6150 |
| 30th | 62 | Haruki Kurosawa / Shogo Mitsuyama | Vemac RD408R | Willcom R&D Sport | 1:54.8570 |
| 31st | 27 | Takashi Inoue / Hwang Jin-Woo | Porsche 996 GT3-RSR | Team Shadow | 1:55.0710 |
| 32nd | 2 | Hiroki Katou / Kazuho Takahashi | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:55.0880 |
| 33rd | 81 | Takayuki Aoki / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Team Daishin | 1:55.1530 |
| 34th | 26 | Shin'ichi Yamaji / Nobuteru Taniguchi | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 1:55.1970 |
| 35th | 66 | Kouji Yamanishi / Atsushi Yogou | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:55.2390 |
| 36th | 52 | Takuya Kurosawa / Takuto Iguchi | Lexus IS350 (GSE21) | Team Takeuchi With Shift | 1:55.2430 |
| 37th | 87 | Muneyuki Kurihara / Hisashi Wada | Lamborghini Gallardo RG-3 | JLOC | 1:55.8190 |
| 38th | 118 | Takshi Miyamoto / Masayuki Kurihara | Porsche 996 GT3-RS | Tomei Sports | 1:55.8210 |
| 39th | 11 | Masayuki Ueda / Tetsuya Tanaka | Ferrari F430 (GF-F360) | Jim Gainer | 1:55.8990 |
| 40th | 111 | Hiroshi Koizumi / Tsubasa Kurosawa | Porsche 986 Boxster | Arktech Motorsports | 1:56.4150 |
| 41st | 666 | Syougo Suhou / Jun'ichirou Yamashita | Vemac RD320R | Avanzza Rosso | 1:56.5930 |
| 42nd | 16 | Tadao Uematsu / Katsuhiko Tsutsui | Vemac RD350R | Team Uematsu Nova | 1:56.9340 |
| 43rd | 9 | Tatsuya Tanigawa / Hirofumi Takei | Chevrolet Corvette C6 (GH-X245) | A&S Racing | no time |