| 36 | Kazuki Nakajima / James Rossiter | Lexus RC F | Lexus Team Petronas Tom's | 1:48.6330 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:48.8460 |
| 23 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R (R35) | NISMO | 1:48.9790 |
| 46 | Satoshi Motoyama / Masataka Yanagida | Nissan GT-R (R35) | Mola | 1:49.3530 |
| 8 | Vitantonio Liuzzi / Kousuke Matsuura | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:49.4030 |
| 12 | Hironobu Yasuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:49.4330 |
| 18 | Naoki Yamamoto / Frédéric Makowiecki | Honda NSX Concept-GT (NSX-P) | weider Modulo Dome Racing | 1:49.5710 |
| 100 | Takashi Kogure / Hideki Mutou | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:55.7080 |
| 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:59.1150 |
| 0 | Yuuki Nakayama / Tomoki Nojiri / Ryou Michigami | Honda CR-Z (ZF2) | Team Mugen | 1:59.6390 |
| 31 | Morio Nitta / Kouki Saga / Yuichi Nakayama | Toyota Prius (ZVW30) | Apr | 1:59.6670 |
| 61 | Kota Sasaki / Takuto Iguchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 2:00.0340 |
| 3 | Kazuki Hoshino / Lucas Ordoñez / Wolfgang Reip | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 2:00.4220 |
| 60 | Akira Iida / Hiroki Yoshimoto / Shin'ya Satou | BMW Z4 GT3 (E89) | LM Corsa | 2:00.9490 |
| 7 | Augusto Farfus / Seiji Ara / Jörg Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 2:01.4150 |
| 65 | Haruki Kurosawa / Tsubasa Kurosawa | Mercedes-Benz SLS AMG GT3 | Leon Racing | 2:01.6680 |
| 10 | Masayuki Ueda / Hideki Yamauchi | Mercedes-Benz SLS AMG GT3 | Gainer | 2:02.1440 |
| 9 | Takuya Shirasaka / André Couto / Taiyo Iida | Porsche 997 GT3 R | Pacific Direction Racing | 2:02.3640 |
| 50 | Masaki Kano / Hideto Yasuoka / Nanin Indra-Payoong | Aston Martin V12 Vantage GT3 | Arnage Racing | 2:02.3920 |