| 38 | Yuuji Tachikawa / Kouhei Hirate | Lexus SC430 (UZZ40) | Lexas Team Zent Cerumo | 1:32.5480 |
| 37 | Daisuke Itou / Andrea Caldarelli | Lexus SC430 (UZZ40) | Lexus Team KeePer Tom's | 1:32.8200 |
| 18 | Naoki Yamamoto / Frédéric Makowiecki | Honda HSV-010 GT (H010) | weider Modulo Dome Racing | 1:32.8240 |
| 100 | Takuya Izawa / Takashi Kogure | Honda HSV-010 GT (H010) | Team Kunimitsu | 1:32.8420 |
| 36 | Kazuki Nakajima / James Rossiter | Lexus SC430 (UZZ40) | Lexus Team Petronas Tom's | 1:32.9250 |
| 6 | Kazuya Oshima / Yuuji Kunimoto | Lexus SC430 (UZZ40) | Lexus Team Le Mans Eneos | 1:33.0470 |
| 1 | Satoshi Motoyama / Yuuhi Sekiguchi | Nissan GT-R (R35) | Mola | 1:33.0620 |
| 17 | Koudai Tsukakoshi / Toshihiro Kaneishi | Honda HSV-010 GT (H010) | Keihin Real Racing | 1:33.2710 |
| 55 | Shinichi Takagi / Takashi Kobayashi | Honda CR-Z (ZF2) | Autobacs Racing Team Aguri | 1:38.7730 |
| 3 | Kazuki Hoshino / Daiki Sasaki | Nissan GT-R Nismo GT3 (R35) | NDDP Racing | 1:39.1980 |
| 16 | Hideki Mutou / Yuuki Nakayama | Honda CR-Z (ZF2) | Team Mugen | 1:39.2370 |
| 61 | Tetsuya Yamano / Kota Sasaki | Subaru BRZ GT300 (DBA-ZC6) | R&D Sport | 1:39.4030 |
| 4 | Nobuteru Taniguchi / Tatsuya Kataoka | BMW Z4 GT3 (E89) | GSR & Studie With Team Ukyo | 1:39.5980 |
| 11 | Katsuyuki Hiranaka / Björn Wirdheim | Mercedes-Benz SLS AMG GT3 | Gainer | 1:39.6440 |
| 5 | Tetsuji Tamanaka / Jun'ichirou Yamashita | Nissan GT-R Nismo GT3 (R35) | Team Mach | 1:39.8730 |
| 10 | Tetsuya Tanaka / Masayuki Ueda | Mercedes-Benz SLS AMG GT3 | Gainer | 1:39.9590 |
| 31 | Morio Nitta / Kouki Saga | Toyota Prius (ZVW30) | Apr | 1:40.0650 |
| 30 | Yuuki Iwasaki / Igor Sushko | Nissan GT-R Nismo GT3 (R35) | Apr | 1:40.1910 |
| 2 | Kazuho Takahashi / Hiroki Katou | McLaren MP4-12C GT3 | Cars Tokai Dream28 | 1:41.2520 |
| 48 | Hiroshi Takamori / Katsumasa Chiyo | Nissan GT-R Nismo GT3 (R35) | Dijon Racing | 1:41.6360 |
| 9 | Shogo Mitsuyama / Yuu Yokomaku | Porsche 997 GT3 R | Pacific Direction Racing | 1:41.9050 |