| 1st | 32 | Duval / Hiranaka | Honda NSX (LA-NA2) | Nakajima Racing | 1:55.470 | 2:10.2410 | | 1:55.4700 | 1:56.9150 |
| 2nd | 1 | Firman / Izawa | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:55.918 | 2:08.4570 | 1:57.8970 | 1:55.9180 | 1:56.7640 |
| 3rd | 12 | Matsuda / Philippe | Nissan GT-R | Team Impul | 1:56.487 | 2:08.7060 | | 1:56.4870 | 1:57.6660 |
| 4th | 22 | Krumm / Schwager / Yanagida | Nissan GT-R | Nismo | 1:56.552 | 2:07.7530 | | 1:57.1130 | 1:56.5520 |
| 5th | 36 | van Dam / Lotterer / Wakisaka | Lexus SC430 (UZZ40) | Petronas Toyota Team Tom's | 1:56.761 | 2:08.7550 | | 1:56.7700 | 1:56.7610 |
| 6th | 100 | Ide / Hosokawa / Matsuura | Honda NSX (LA-NA2) | Team Kunimitsu | 1:56.783 | 2:07.4740 | 1:58.2660 | 1:56.7830 | 1:57.3250 |
| 7th | 3 | Quintarelli / Yokomizo | Nissan GT-R | Hasemi Motorsport | 1:57.139 | 2:12.0580 | | 1:57.1390 | 1:57.3940 |
| 8th | 23 | Tréluyer / Motoyama / Carbone | Nissan GT-R | Nismo | 1:57.158 | 2:08.9840 | | 1:57.1580 | 1:57.2180 |
| 9th | 24 | de Oliveira / Ara | Nissan GT-R | Kondo Racing | 1:57.422 | 2:11.5140 | | 1:57.4220 | 1:58.0840 |
| 10th | 6 | Iida / Streit / Wirdheim | Lexus SC430 (UZZ40) | Eneos Toyota Team Le Mans | 1:57.505 | 2:09.0460 | | 1:58.5720 | 1:57.5050 |
| 11th | 17 | Kaneishi / Kaneishi / Tsukakoshi | Honda NSX (LA-NA2) | Real Racing With Leon | 1:57.506 | 2:08.4210 | | 1:57.7850 | 1:57.5060 |
| 12th | 39 | Couto / Takagi / Saga | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:57.600 | 2:10.3590 | | 1:57.6000 | 1:58.1640 |
| 13th | 18 | Michigami / Kogure | Honda NSX (LA-NA2) | Dome Racing Team | 1:57.860 | 2:09.1120 | | 1:57.8900 | 1:57.8600 |
| 14th | 35 | Kataoka / Dumbreck | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:57.945 | 2:08.9170 | | 1:58.2840 | 1:57.9450 |
| 15th | 25 | Tsuchiya / Ishiura | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:57.959 | 2:11.9610 | | 1:57.9590 | 2:00.5850 |
| 16th | 38 | Tachikawa / Lyons | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:58.035 | 2:09.1440 | 1:58.2400 | 1:58.0350 | 1:59.2840 |
| 17th | 2 | Katou / Takahashi / Yoshimoto | Shiden MC/RT-16 | Cars Tokai Dream28 | 2:07.411 | 2:23.9190 | | 2:07.4110 | 2:08.6820 |
| 18th | 4 | Sakaguchi / Matsushita / Uematsu | Vemac RD320R | Team Uematsu Nova | 2:08.411 | 2:25.9890 | | 2:08.4110 | 2:09.8220 |
| 19th | 26 | Taniguchi / Yamaji / Sawa | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 2:08.429 | 2:26.1660 | 2:10.1550 | 2:08.4290 | 2:09.1560 |
| 20th | 19 | Orido / Abe / Sekiguchi | Lexus IS350 (GSE21) | Racing Project Bandoh | 2:08.527 | 2:24.4180 | 2:09.3400 | 2:09.8580 | 2:08.5270 |
| 21st | 43 | Takagi / Nitta / Mineo | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 2:08.528 | 2:23.2710 | | 2:08.5280 | 2:10.0240 |
| 22nd | 11 | Tanaka / Ueda | Ferrari F430 (GF-F360) | Jim Gainer | 2:08.608 | 2:25.5750 | | 2:08.6080 | 2:08.8660 |
| 23rd | 46 | Hoshino / Yasuda | Nissan Fairlady Z (Z33) | Mola | 2:08.628 | 2:24.0640 | | 2:08.6280 | 2:08.7830 |
| 24th | 7 | Iiri / Orime / Matsumura | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:08.867 | 2:26.3970 | | 2:08.8670 | 2:09.6820 |
| 25th | 81 | Fujii / Aoki | Nissan Fairlady Z (Z33) | Team Daishin | 2:08.873 | 2:24.9200 | | 2:09.5850 | 2:08.8730 |
| 26th | 52 | Kurosawa / Iguchi / Yamauchi | Lexus IS350 (GSE21) | Team Takeuchi With Shift | 2:09.061 | 2:27.6520 | | 2:09.2120 | 2:09.0610 |
| 27th | 62 | Kurosawa / Shibahara / Mitsuyama | Vemac RD408R | Willcom R&D Sport | 2:09.092 | 2:28.2090 | | 2:09.0920 | 2:09.4150 |
| 28th | 95 | Oshima / Kunimoto / Sakamoto | Toyota MR-S (GH-ZZW30) | Apr | 2:09.412 | 2:23.5830 | 2:10.2210 | 2:09.5550 | 2:09.4120 |
| 29th | 77 | Sasaki / Yamano | Subaru Impreza (GD) | Cusco Racing | 2:09.523 | 2:22.4320 | | 2:10.7030 | 2:09.5230 |
| 30th | 5 | Tamanaka / Yamano / Tsutsui | Vemac RD320R | Team Mach | 2:09.954 | 2:29.6060 | | 2:10.4380 | 2:09.9540 |
| 31st | 33 | Kinoshita / Kageyama | Porsche 997 GT3 RSR | Hankook KTR | 2:10.210 | 2:25.8200 | | 2:10.2100 | 2:10.5750 |
| 32nd | 66 | Yamanishi / Yogou | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 2:10.948 | 2:25.1580 | | 2:10.9480 | 2:11.9720 |
| 33rd | 111 | Kurosawa / Koizumi | Porsche 986 Boxster | Arktech Motorsports | 2:11.149 | 2:30.1950 | | 2:11.4950 | 2:11.1490 |
| 34th | 118 | Jounai / Miyamoto / Kurihara | Porsche 996 GT3-RS | Tomei Sports | 2:11.263 | 2:28.6990 | | 2:11.2630 | 2:14.5240 |
| 35th | 27 | Inoue / Jin-Woo / Takasaki | Porsche 996 GT3-RSR | Team Shadow | 2:11.676 | no time | | 2:11.8590 | 2:11.6760 |
| 36th | 87 | Wada / Kurihara / Namekata | Lamborghini Gallardo RG-3 | JLOC | 2:11.726 | 2:28.2190 | | 2:11.7260 | 2:13.2860 |
| 37th | 88 | Matsuda / Furuya / Sakamoto | Lamborghini Gallardo RG-3 | JLOC | 2:11.745 | 2:27.1070 | | 2:11.7450 | 2:13.6990 |
| 38th | 666 | Suhou / Yamashita / "Takamori.com" | Vemac RD320R | Avanzza Rosso | 2:12.003 | 2:30.8960 | | 2:12.0030 | 2:12.6780 |
| 39th | 170 | Yamagishi / Ishibashi / Takamizawa | Porsche 996 GT3-RS | Team Gaikokuya | 2:12.440 | 2:31.4400 | | 2:12.4400 | 2:16.6200 |
| 40th | 110 | Mitsusada / Ikeda | Porsche 986 Boxster | Arktech Motorsports | 2:13.096 | 2:42.3170 | | 2:15.0360 | 2:13.0960 |
| 41st | 9 | Tanigawa / Takei / Matsumoto | Chevrolet Corvette C6 (GH-X245) | A&S Racing | 2:16.959 | 2:40.2810 | | no time | 2:16.9590 |
| 42nd | 808 | Kikuchi / Tagahara | BMW Z4 M Coupe (S62) | Studie & Glad With Asada Racing | 2:19.225 | no time | | 2:38.9590 | 2:19.2250 |