| 23 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R (R35) | NISMO | 1:38.2580 |
| 46 | Satoshi Motoyama / Masataka Yanagida | Nissan GT-R (R35) | Mola | 1:38.5920 |
| 18 | Naoki Yamamoto / Takuya Izawa | Honda NSX Concept-GT (NSX-P) | weider Modulo Dome Racing | 1:38.8810 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus RC F | Lexus Team Petronas Tom's | 1:38.9560 |
| 12 | Hironobu Yasuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:39.0130 |
| 32 | Daisuke Nakajima / Bertrand Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:39.2240 |
| 19 | Juichi Wakisaka / Yuuhi Sekiguchi | Lexus RC F | Lexus Team WedsSport Bandoh | 1:39.7710 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:40.0500 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:47.7960 |
| 31 | Morio Nitta / Kouki Saga | Toyota Prius (ZVW30) | Apr | 1:47.9770 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:48.5000 |
| 65 | Haruki Kurosawa / Naoya Gamou | Mercedes-Benz SLS AMG GT3 | Leon Racing | 1:48.5620 |
| 0 | Yuuki Nakayama / Tomoki Nojiri | Honda CR-Z (ZF2) | Team Mugen | 1:48.5830 |
| 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:48.7470 |
| 3 | Kazuki Hoshino / Lucas Ordoñez | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:48.9790 |
| 10 | Masayuki Ueda / Hideki Yamauchi | Mercedes-Benz SLS AMG GT3 | Gainer | 1:49.0760 |
| 21 | Richard Lyons / Tomonobu Fujii | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:49.0910 |
| 86 | Shin'ya Hosokawa / Kouji Yamanishi | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:49.3380 |
| 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 1:49.3820 |
| 9 | Takuya Shirasaka / Yuuya Sakamoto | Porsche 997 GT3 R | Pacific Direction Racing | 1:50.2110 |
| 2 | Kazuho Takahashi / Hiroki Katou | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 1:51.2900 |