| 1st | 23 | Benoit Tréluyer / Satoshi Motoyama | Nissan GT-R | Nismo | 1:41.5200 |
| 2nd | 1 | Ralph Firman / Takuya Izawa | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:43.6030 |
| 3rd | 32 | Loïc Duval / Katsuyuki Hiranaka | Honda NSX (LA-NA2) | Nakajima Racing | 1:41.2260 |
| 4th | 18 | Takashi Kogure / Ryō Michigami | Honda NSX (LA-NA2) | Dome Racing Team | 1:41.5580 |
| 5th | 3 | Ronnie Quintarelli / Naoki Yokomizo | Nissan GT-R | Hasemi Motorsport | 1:41.9600 |
| 6th | 35 | Tatsuya Kataoka / Peter Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:42.6220 |
| 7th | 36 | Andre Lotterer / Juichi Wakisaka | Lexus SC430 (UZZ40) | Petronas Toyota Team Tom's | 1:41.9810 |
| 8th | 100 | Yuuji Ide / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 1:42.4250 |
| 9th | 25 | Takeshi Tsuchiya / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:42.3570 |
| 10th | 38 | Yuji Tachikawa / Richard Lyons | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:42.2630 |
| 11th | 17 | Toshihiro Kaneishi / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Real Racing With Leon | 1:42.8080 |
| 12th | 6 | Akira Iida / Björn Wirdheim | Lexus SC430 (UZZ40) | Eneos Toyota Team Le Mans | 1:43.8000 |
| 13th | 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan GT-R | Kondo Racing | 1:43.9620 |
| 14th | 12 | Tsugio Matsuda / Sébastien Philippe | Nissan GT-R | Team Impul | 1:44.7400 |
| 15th | 39 | André Couto / Toranosuke Takagi | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:42.3040 |
| 16th | 22 | Michael Krumm / Masataka Yanagida | Nissan GT-R | Nismo | no time |
| 17th | 11 | Tetsuya Tanaka / Masayuki Ueda | Ferrari F430 (GF-F360) | Jim Gainer | 1:51.5050 |
| 18th | 81 | Takayuki Aoki / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Team Daishin | 1:52.0280 |
| 19th | 2 | Hiroki Kato / Kazuho Takahashi | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:51.6150 |
| 20th | 19 | Manabu Orido / Tsubasa Abe | Lexus IS350 (GSE21) | Racing Project Bandoh | 1:52.2130 |
| 21st | 26 | Nobuteru Taniguchi / Shinichi Yamaji | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 1:52.0370 |
| 22nd | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:52.1890 |
| 23rd | 62 | Haruki Kurosawa / Shinsuke Shibahara | Vemac RD408R | Willcom R&D Sport | 1:52.5780 |
| 24th | 46 | Kazuki Hoshino / Hironobu Yasuda | Nissan Fairlady Z (Z33) | Mola | 1:52.4210 |
| 25th | 33 | Masami Kageyama / Mitsuhiro Kinoshita | Porsche 997 GT3 RSR | Hankook KTR | 1:52.5400 |
| 26th | 4 | Ryohei Sakaguchi / Masaki Matsushita | Vemac RD320R | Team Uematsu Nova | 1:52.3010 |
| 27th | 52 | Takuya Kurosawa / Takuto Iguchi | Lexus IS350 (GSE21) | Team Takeuchi With Shift | 1:52.7740 |
| 28th | 110 | Hidetoshi Mitsusada / Daisuke Ikeda | Porsche 986 Boxster | Arktech Motorsports | 1:52.9000 |
| 29th | 31 | Yuuya Sakamoto / Kyousuke Mineo | Toyota MR-S (GH-ZZW30) | Apr | 1:52.9080 |
| 30th | 77 | Carlo van Dam / Tetsuya Yamano | Subaru Impreza (GD) | Cusco Racing | 1:52.9480 |
| 31st | 7 | Hiroyuki Iiri / Ryou Orime | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:53.0160 |
| 32nd | 95 | Keisuke Kunimoto / Kouhei Hirate | Toyota MR-S (GH-ZZW30) | Apr | 1:53.0650 |
| 33rd | 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 1:53.1960 |
| 34th | 88 | Hideshi Matsuda / Naohiro Furuya | Lamborghini Gallardo RG-3 | JLOC | 1:53.6180 |
| 35th | 66 | Koji Yamanishi / Atsushi Yogo | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:53.6870 |
| 36th | 111 | Tsubasa Kurosawa / Hiroshi Koizumi | Porsche 986 Boxster | Arktech Motorsports | 1:53.8100 |
| 37th | 87 | Muneyuki Kurihara / Hisashi Wada | Lamborghini Gallardo RG-3 | JLOC | 1:54.5770 |
| 38th | 118 | Takshi Miyamoto / Masaki Jounai | Porsche 996 GT3-RS | Tomei Sports | 1:54.7880 |
| 39th | 666 | Syougo Suhou / Jun'ichirou Yamashita | Vemac RD320R | Avanzza Rosso | 1:55.6420 |