| 39 | Hiroaki Ishiura / Oliver Jarvis | Lexus RC F | Lexus Team Sard | 1:29.9860 |
| 23 | Tsugio Matsuda / Ronnie Quintarelli | Nissan GT-R (R35) | NISMO | 1:30.0100 |
| 18 | Naoki Yamamoto / Frédéric Makowiecki | Honda NSX Concept-GT (NSX-P) | weider Modulo Dome Racing | 1:30.0610 |
| 24 | Michael Krumm / Daiki Sasaki | Nissan GT-R (R35) | Kondo Racing | 1:30.1030 |
| 8 | Vitantonio Liuzzi / Kousuke Matsuura | Honda NSX Concept-GT (NSX-P) | Autobacs Racing Team Aguri | 1:30.1760 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus RC F | Lexus Team Petronas Tom's | 1:30.3360 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda NSX Concept-GT (NSX-P) | Keihin Real Racing | 1:30.4300 |
| 100 | Takashi Kogure / Hideki Mutou | Honda NSX Concept-GT (NSX-P) | Team Kunimitsu | 1:30.4530 |
| 19 | Juichi Wakisaka / Yuuhi Sekiguchi | Lexus RC F | Lexus Team WedsSport Bandoh | 1:30.4630 |
| 12 | Hironobu Yasuda / Joao Paolo de Oliveira | Nissan GT-R (R35) | Team Impul | 1:30.5010 |
| 32 | Daisuke Nakajima / Bertrand Baguette | Honda NSX Concept-GT (NSX-P) | Nakajima Racing | 1:30.5810 |
| 1 | Yuuji Tachikawa / Kouhei Hirate | Lexus RC F | Lexus Team Zent Cerumo | 1:30.6730 |
| 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus RC F | Lexus Team Le Mans Eneos | 1:30.8040 |
| 37 | Daisuke Itou / Andrea Caldarelli | Lexus RC F | Lexus Team KeePer Tom's | 1:31.1710 |
| 46 | Satoshi Motoyama / Masataka Yanagida | Nissan GT-R (R35) | Mola | 1:31.2320 |
| 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:38.1760 |
| 0 | Yuuki Nakayama / Tomoki Nojiri | Honda CR-Z (ZF2) | Team Mugen | 1:38.2780 |
| 2 | Kazuho Takahashi / Hiroki Katou | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 1:38.7480 |
| 10 | Masayuki Ueda / Hideki Yamauchi | Mercedes-Benz SLS AMG GT3 | Gainer | 1:38.8620 |
| 360 | Atsushi Tanaka / Hiroki Yoshida | Nissan GT-R Nismo GT3 (R35) | Tomei Sports | 1:38.9490 |
| 3 | Kazuki Hoshino / Lucas Ordoñez | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:38.9830 |
| 86 | Shin'ya Hosokawa / Kouji Yamanishi | Lamborghini Gallardo GT3 (09-7) | JLOC | 1:39.0370 |
| 61 | Kota Sasaki / Takuto Iguchi | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:39.0600 |
| 7 | Seiji Ara / Jörg Müller | BMW Z4 GT3 (E89) | BMW Sports Trophy Team Studie | 1:39.2510 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:39.3260 |
| 31 | Morio Nitta / Kouki Saga | Toyota Prius (ZVW30) | Apr | 1:39.3670 |
| 65 | Haruki Kurosawa / Tsubasa Kurosawa | Mercedes-Benz SLS AMG GT3 | Leon Racing | 1:39.3840 |
| 30 | Yuuki Iwasaki / Masami Kageyama | Nissan GT-R Nismo GT3 (R35) | Apr | 1:39.4480 |
| 33 | Akihiro Tsuduki / Kyousuke Mineo | Porsche 997 GT3 R | Porsche Team KTR | 1:39.5360 |
| 60 | Akira Iida / Hiroki Yoshimoto | BMW Z4 GT3 (E89) | LM Corsa | 1:39.5600 |
| 67 | Naoki Yokomizo / Shogo Mitsuyama | Nissan GT-R Nismo GT3 (R35) | Team Taisan | 1:39.5990 |
| 5 | Tetsuji Tamanaka / Jun'ichirou Yamashita | Nissan GT-R Nismo GT3 (R35) | Team Mach | 1:39.8090 |
| 50 | Masaki Kano / Hideto Yasuoka | Aston Martin V12 Vantage GT3 | Arnage Racing | 1:39.8980 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:39.9600 |
| 9 | Takuya Shirasaka / André Couto | Porsche 997 GT3 R | Pacific Direction Racing | 1:40.2100 |
| 88 | Manabu Orido / Takayuki Aoki | Lamborghini Gallardo GT3 (22-12226) | JLOC | 1:40.3760 |
| 48 | Hiroshi Takamori / Masaki Tanaka | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:40.9250 |
| 21 | Richard Lyons / Tomonobu Fujii | Audi R8 LMS Ultra | Audi Team Hitotsuyama | 1:42.0660 |