| 1st | 32 | Loic Duval / Yuuki Nakayama | Honda NSX (LA-NA2) | Nakajima Racing | 1:45.8420 |
| 2nd | 1 | Satoshi Motoyama / Benoit Tréluyer | Nissan GT-R (R35) | Nismo | 1:46.0660 |
| 3rd | 36 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:46.3620 |
| 4th | 6 | Daisuke Itou / Björn Wirdheim | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:46.2710 |
| 5th | 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan GT-R (R35) | Kondo Racing | 1:46.3140 |
| 6th | 12 | Tsugio Matsuda / Sébastien Philippe | Nissan GT-R (R35) | Team Impul | 1:46.0320 |
| 7th | 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Yoshiki & Dome Project | 1:46.2230 |
| 8th | 100 | Yuuji Ide / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 1:46.4750 |
| 9th | 17 | Toshihiro Kaneishi / Koudai Tsukakoshi | Honda NSX (LA-NA2) | Keihin Real Racing | 1:46.7190 |
| 10th | 35 | Kazuya Oshima / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Kraft | 1:46.9910 |
| 11th | 39 | André Couto / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:47.0840 |
| 12th | 8 | Ralph Firman / Takuya Izawa | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:46.1820 |
| 13th | 38 | Yuuji Tachikawa / Richard Lyons | Lexus SC430 (UZZ40) | Lexus Team Zent Cerumo | 1:47.2530 |
| 14th | 3 | Ronnie Quintarelli / Hironobu Yasuda | Nissan GT-R (R35) | Hasemi Motor Sport | 1:47.8810 |
| 15th | 21 | Akihiro Tsuduki / Takeshi Tsuchiya | Aston Martin DBR9 | Team Nova | 1:48.9490 |
| 17th | 88 | Hideshi Matsuda / Yuuya Sakamoto | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:55.9690 |
| 18th | 81 | Takayuki Aoki / Tomonobu Fujii | Ferrari F430 | Team Daishin | 1:56.3060 |
| 19th | 33 | Mitsuhiro Kinoshita / Masami Kageyama | Porsche 997 GT3 RSR | Hankook KTR | 1:55.3570 |
| 20th | 87 | Hiroyuki Iiri / Hisashi Wada | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:56.3600 |
| 21st | 46 | Kazuki Hoshino / Masataka Yanagida | Nissan Fairlady Z (Z33) | Team Nishizawa Mola | 1:56.3050 |
| 22nd | 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:56.9830 |
| 23rd | 74 | Takuto Iguchi / Yuuji Kunimoto | Toyota Corolla Axio (NZE141) | Apr | 1:56.4600 |
| 24th | 26 | Haruki Kurosawa / Tsubasa Abe | Porsche 996 GT3-RS | Team Taisan | 1:55.9450 |
| 25th | 19 | Manabu Orido / Tatsuya Kataoka | Lexus IS350 (GSE21) | Racing Project Bandoh | 1:56.7170 |
| 26th | 11 | Tetsuya Tanaka / Katsuyuki Hiranaka | Ferrari F430 (F430SC) | Jim Gainer | 1:56.7920 |
| 27th | 5 | Tetsuji Tamanaka / "Akazame Oyaji" | Vemac RD320R Porsche | Team Mach | 1:56.8590 |
| 28th | 66 | Kouji Yamanishi / Atsushi Yogou | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:56.8920 |
| 29th | 7 | Nobuteru Taniguchi / Ryou Orime | Mazda RX-7 (FD3S) | M7 RE-Amemiya Racing | 1:57.3010 |
| 30th | 2 | Hiroki Katou / Hiroki Yoshimoto | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:57.3890 |
| 31st | 31 | Yuuya Sakamoto / Kyousuke Mineo | Toyota Corolla Axio (NZE141) | Apr | 1:57.7830 |
| 32nd | 808 | Yasushi Kikuchi / Syouzou Tagahara | BMW Z4 M Coupe (E86) | Studie Glad Racing | 1:58.4250 |
| 33rd | 55 | Yutaka Yamagishi / Hiroshi Koizumi | Porsche 996 GT3-RSR | Tomei Sports | 1:58.7220 |
| 34th | 52 | Kota Sasaki / Yuuhi Sekiguchi | Lexus IS350 (GSE21) | Shift | 1:59.0740 |
| 35th | 10 | Masayuki Ueda / Masataka Kawaguchi | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:59.4470 |
| 36th | 112 | Yoshiaki Nakayama / Takashi Ooi | Porsche 996 GT3-RSR | Arktech Motorsports | 2:00.4620 |
| 37th | 62 | Tetsuya Yamano / Shogo Mitsuyama | Subaru Legacy B4 (BM9) | R&D Sport | 2:00.7790 |
| 38th | 666 | Syougo Suhou / Jun'ichirou Yamashita | Vemac RD320R | Avanzza Rosso | 2:03.8530 |