| 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:41.3670 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:41.4900 |
| 23 | Masataka Yanagida / Ronnie Quintarelli | Nissan GT-R (R35) | Nismo | 1:41.5140 |
| 38 | Yuuji Tachikawa / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexas Team Zent Cerumo | 1:41.5820 |
| 39 | Juichi Wakisaka / Hiroaki Ishiura | Lexus SC430 (UZZ40) | Lexus Team Sard | 1:41.5980 |
| 100 | Takuya Izawa / Takashi Kogure | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:42.1440 |
| 37 | Daisuke Itou / Andrea Caldarelli | Lexus SC430 (UZZ40) | Lexus Team KeePer Tom's | 1:42.3230 |
| 12 | Tsugio Matsuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:42.3740 |
| 61 | Tetsuya Yamano / Kota Sasaki | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:48.2640 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:48.3540 |
| 16 | Hideki Mutou / Yuuki Nakayama | Honda CR-Z (ZF2) | Team Mugen | 1:48.3890 |
| 3 | Kazuki Hoshino / Daiki Sasaki | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:48.9000 |
| 62 | Haruki Kurosawa / Tsubasa Kurosawa | Mercedes-Benz SLS AMG GT3 | Leon Racing | 1:48.9700 |
| 88 | Manabu Orido / Takayuki Aoki | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:49.2410 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:49.5180 |
| 87 | Hideki Yamauchi / Hiroki Yoshimoto | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:49.5510 |
| 33 | Masami Kageyama / Tomonobu Fujii | Porsche 997 GT3 R | Hankook KTR | 1:49.6000 |
| 0 | Kyousuke Mineo / Naoki Yokomizo | Porsche 997 GT3 R | Team Taisan Ken Endless | 1:49.7890 |
| 10 | Tetsuya Tanaka / Masayuki Ueda | Mercedes-Benz SLS AMG GT3 | Gainer | 1:50.2400 |
| 2 | Kazuho Takahashi / Hiroki Katou | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 1:52.2380 |
| 48 | Hiroshi Takamori / Katsumasa Chiyo | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:52.2760 |