| 23 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R (R35) | NISMO | 1:39.2580 |
| 46 | Satoshi Motoyama / Masataka Yanagida | Nissan GT-R (R35) | Mola | 1:39.2580 |
| 19 | Juichi Wakisaka / Yuuhi Sekiguchi | Lexus RC F | Lexus Team WedsSport Bandoh | 1:39.3510 |
| 32 | Daisuke Nakajima / Bertrand Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:39.3790 |
| 12 | Hironobu Yasuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:39.3830 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:39.3940 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus RC F | Lexus Team Petronas Tom's | 1:39.5290 |
| 18 | Naoki Yamamoto / Takuya Izawa | Honda NSX Concept-GT (NSX-P) | weider Modulo Dome Racing | 1:39.6900 |
| 100 | Takashi Kogure / Hideki Mutou | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:39.8740 |
| 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus RC F | Lexus Team Le Mans Eneos | 1:40.0450 |
| 39 | Hiroaki Ishiura / Oliver Jarvis | Lexus RC F | Lexus Team Sard | 1:40.5330 |
| 8 | Vitantonio Liuzzi / Kousuke Matsuura | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:40.7510 |
| 37 | Daisuke Itou / Andrea Caldarelli | Lexus RC F | Lexus Team KeePer Tom's | 1:47.5120 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:47.7170 |
| 10 | Masayuki Ueda / Hideki Yamauchi | Mercedes-Benz SLS AMG GT3 | Gainer | 1:48.2400 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:48.4610 |
| 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:48.6000 |
| 3 | Kazuki Hoshino / Lucas Ordoñez | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:48.6250 |
| 65 | Haruki Kurosawa / Naoya Gamou | Mercedes-Benz SLS AMG GT3 | Leon Racing | 1:48.7550 |
| 0 | Yuuki Nakayama / Tomoki Nojiri | Honda CR-Z (ZF2) | Team Mugen | 1:48.7760 |
| 2 | Kazuho Takahashi / Hiroki Katou | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 1:48.9160 |
| 21 | Richard Lyons / Tomonobu Fujii | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:49.0400 |
| 31 | Morio Nitta / Kouki Saga | Toyota Prius (ZVW30) | Apr | 1:49.1750 |
| 22 | Hisashi Wada / Masaki Jounai | Mercedes-Benz SLS AMG GT3 | R'Qs Motorsports | 1:49.2350 |
| 9 | Takuya Shirasaka / Yuuya Sakamoto | Porsche 997 GT3 R | Pacific Direction Racing | 1:49.3740 |
| 86 | Shin'ya Hosokawa / Kouji Yamanishi | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:49.4570 |
| 7 | Seiji Ara / Jörg Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 1:49.6660 |
| 50 | Masaki Kano / Hideto Yasuoka | Aston Martin V12 Vantage GT3 | Arnage Racing | 1:49.7600 |
| 33 | Akihiro Tsuduki / Kyousuke Mineo | Porsche 997 GT3 R | Porsche Team KTR | 1:49.8090 |
| 88 | Manabu Orido / Takayuki Aoki | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:50.0190 |
| 30 | Yuuki Iwasaki / Masami Kageyama | Nissan GT-R Nismo GT3 (R35) | Apr | 1:50.0400 |
| 61 | Kota Sasaki / Takuto Iguchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:50.0520 |
| 67 | Naoki Yokomizo / Shogo Mitsuyama | Nissan GT-R Nismo GT3 (R35) | Team Taisan | 1:50.1260 |
| 360 | Atsushi Tanaka / Hiroki Yoshida | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:50.5580 |
| 48 | Hiroshi Takamori / Masaki Tanaka | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:51.6850 |
| 60 | Hiroki Yoshimoto / Shin'ya Satou | BMW Z4 GT3 (E89) | LM Corsa | 2:26.5870 |
| 24 | Michael Krumm / Daiki Sasaki | Nissan GT-R (R35) | Kondo Racing | 4:23.5760 |