Yamashita, replacing Nick Cassidy in the #37 Toyota GR Supra alongside Ryo Hirakawa for the final two races of the season, posted a 1m26.386s at the end of the Q2 pole shootout to score a vital bonus point for Hirakawa's championship quest.
That was half a tenth underneath the record established by Honda man Nirei Fukuzumi during qualifying for the opening race of the year at Fuji.
Yamashita had topped practice earlier in the day, while Hirakawa set the pace in Q1 to give the #37 car a clean sweep during Saturday's track action.
A second pole of the season gives Hirakawa a one-point lead over Real Racing Honda pair Bertrand Baguette and Koudai Tsukakoshi heading into Sunday's decider.
Heikki Kovalainen gave the SARD Toyota squad its best grid slot of the season in second, albeit 0.367s behind Yamashita, while Yuhi Sekiguchi in the #36 TOM'S Supra and Yuji Tachikawa in the #38 Cerumo car will line up on the second row.
Best of the non-Toyotas was the Nakajima Racing Honda of Takuya Izawa in fifth, followed by top Nissan driver and title contender Ronnie Quintarelli in sixth.
Rounding out the Q2 order were Naoki Yamamoto in the Team Kunimitsu Honda team's final outing with long-time sponsor Raybrig, and Kazuki Hiramine in the Impul Nissan GT-R.
Honda lost two of its three realistic title contenders in Q1 as Tomoki Nojiri could only manage 11th in the ARTA NSX-GT, and Baguette was 12th in the Real Racing car.
Also suffering a qualifying session to forget was the #14 Cerumo Toyota, which was 13th-fastest in the hands of reigning champion Kazuya Oshima.
GT300: Saitama Toyopet boosts title bid with pole
The Saitama Toyopet team's outside hopes of securing the GT300 title were given a boost when Kohta Kawaii took pole in the Toyota GR Supra GT300 he shares with Hiroki Yoshida.
Kawaii set a 1m34.665s to beat the class lap record by more than a second and take pole by over four tenths from the works Subaru BRZ of Takuto Iguchi and Hideki Yamauchi, which also heads into the final race with ambitions of clinching the crown.
It means Kawaii and Yoshida head into the finale 14 points adrift of the Kondo Racing Nissan GT-R NISMO GT3 of Joao Paulo de Oliveira and Kiyoto Fujinami, who qualified seventh.
The second-best of the title contenders, the LEON Racing Mercedes-AMG GT3 of Naoya Gamou and Togo Suganami, was fifth behind the Inging Motorsport Toyota GT86 MC and the K-tunes Racing Lexus RC F GT3, both of which are out of the reckoning.
Gamou and Suganami trail de Oliveira and Fujinami by five points, meaning the latter pair could afford to finish second behind the Mercedes and claim the title on countback.
Splitting the two cars on the grid will be the #11 Gainer Nissan, whose drivers Katsuyuki Hiranaka and Hironobu Yasuda are 13 points off the head of the standings.
The sixth and final championship-contending car, the ARTA Honda NSX GT3 of Toshiki Oyu and Nobuharu Matsushita, will start from the back row following engine trouble during practice.
GT500 qualifying results:
Pos. | No. | Team/Car | Drivers | Q1 | Q2 |
---|---|---|---|---|---|
1 | 37 | TOM'S Toyota |
| 1m26.722s | 1m26.386s |
2 | 39 | SARD Toyota |
| 1m27.071s | 1m26.753s |
3 | 36 | TOM'S Toyota |
| 1m26.790s | 1m26.841s |
4 | 38 | Cerumo Toyota |
| 1m27.046s | 1m27.039s |
5 | 64 | Nakajima Honda |
| 1m27.175s | 1m27.113s |
6 | 23 | NISMO Nissan |
| 1m27.188s | 1m27.130s |
7 | 100 | Kunimitsu Honda |
| 1m27.324s | 1m27.229s |
8 | 12 | Impul Nissan |
| 1m27.379s | 1m27.647s |
9 | 3 | NDDP/B-Max Nissan |
| 1m27.414s | |
10 | 19 | Bandoh Toyota |
| 1m27.417s | |
11 | 8 | ARTA Honda |
| 1m27.508s | |
12 | 17 | Real Racing Honda |
| 1m27.579s | |
13 | 14 | Cerumo Toyota |
| 1m27.723s | |
14 | 16 | Mugen Honda |
| 1m28.081s | |
15 | 24 | Kondo Nissan |
| 1m28.555s |