| 38 | Yuuji Tachikawa / Richard Lyons | Lexus SC430 (UZZ40) | Lexus Team Zent Cerumo | 1:25.5200 |
| 6 | Daisuke Itou / Björn Wirdheim | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:25.7460 |
| 3 | Ronnie Quintarelli / Hironobu Yasuda | Nissan GT-R (R35) | Hasemi Motor Sport | 1:25.9260 |
| 12 | Tsugio Matsuda / Sébastien Philippe | Nissan GT-R (R35) | Team Impul | 1:25.9840 |
| 24 | Joao Paolo de Oliveira / Seiji Ara | Nissan GT-R (R35) | Kondo Racing | 1:26.0610 |
| 35 | Kazuya Oshima / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Kraft | 1:26.1020 |
| 36 | Juichi Wakisaka / Andre Lotterer | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:26.1270 |
| 18 | Ryou Michigami / Takashi Kogure | Honda NSX (LA-NA2) | Team Yoshiki & Dome Project | 1:26.1420 |
| 39 | André Couto / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:26.1510 |
| 8 | Ralph Firman / Takuya Izawa | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:26.2500 |
| 32 | Loïc Duval / Yuuki Nakayama | Honda NSX (LA-NA2) | Nakajima Racing | 1:26.2590 |
| 1 | Satoshi Motoyama / Benoit Tréluyer | Nissan GT-R (R35) | Nismo | 1:26.2670 |
| 17 | Toshihiro Kaneishi / Koudai Tsukakoshi / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Keihin Real Racing | 1:26.6770 |
| 100 | Yuuji Ide / Shin'ya Hosokawa | Honda NSX (LA-NA2) | Team Kunimitsu | 1:27.1660 |
| 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (GT300VQ) | Autobacs Racing Team Aguri | 1:32.5440 |
| 46 | Kazuki Hoshino / Masataka Yanagida | Nissan Fairlady Z (Z33) | Team Nishizawa Mola | 1:32.5980 |
| 19 | Manabu Orido / Tatsuya Kataoka | Lexus IS350 (GSE21) | Racing Project Bandoh | 1:32.6060 |
| 2 | Kazuho Takahashi / Hiroki Katou | Shiden MC/RT-16 | Cars Tokai Dream28 | 1:32.7970 |
| 88 | Hideshi Matsuda / Naohiro Furuya / Yuuya Sakamoto | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:32.9420 |
| 7 | Nobuteru Taniguchi / Ryou Orime / Charles Lowe | Mazda RX-7 (FD3S) | M7 RE-Amemiya Racing | 1:33.0780 |
| 26 | Haruki Kurosawa / Tsubasa Abe | Porsche 996 GT3-RS | Team Taisan | 1:33.3570 |
| 66 | Kouji Yamanishi / Atsushi Yogou / Tetsuya Yamano | Lamborghini Murcielago RG-1 (GH-BC10E) | JLOC | 1:33.4400 |
| 11 | Tetsuya Tanaka / Katsuyuki Hiranaka | Ferrari F430 (F430SC) | Jim Gainer | 1:33.6310 |
| 81 | Takayuki Aoki / Tomonobu Fujii | Ferrari F430 | Team Daishin | 1:33.6720 |
| 30 | Kota Sasaki / Kousuke Matsuura | Lexus IS350 (GSE21) | Team Reckless With Shift | 1:33.7960 |
| 87 | Hisashi Wada / Hiroyuki Iiri | Lamborghini Gallardo RG-3 (ZHWGE) | JLOC | 1:33.8040 |
| 5 | Tetsuji Tamanaka / "Akazame Oyaji" | Vemac RD320R Porsche | Team Mach | 1:33.8090 |
| 74 | Takuto Iguchi / Yuuji Kunimoto | Toyota Corolla Axio (NZE141) | Apr | 1:34.2500 |
| 10 | Masayuki Ueda / Masataka Kawaguchi | Ferrari 360 Modena (GF-F360) | Jim Gainer | 1:34.6390 |
| 31 | Yuuya Sakamoto / Hideki Yamauchi / "Takamori.com" | Toyota Corolla Axio (NZE141) | Apr | 1:34.7390 |
| 666 | Syougo Suhou / Jun'ichirou Yamashita | Vemac RD320R | Avanzza Rosso | 1:36.1980 |