Lexus locked out the front-row in qualifying for Super GT's Thailand round, as Jenson Button and Naoki Yamamoto claimed the honour of being the top Honda drivers in seventh.
It was TOM'S Lexus driver Kazuki Nakajima who set the first competitive lap in Q2, clocking a time of 1m23.457s to go to the top of the timesheets.
Nakajima was almost immediately dislodged from the premier spot by the Bandoh Lexus of Yuji Kunimoto, the 2016 Super Formula champion nearly eclipsing the track record of 1m23.341s.
In the end, however, it was Yamashita who secured surprise pole position in the Lexus he shares with Kazuya Oshima with a time of 1m23.260s.
Kunimoto's previous time of 1m23.350s was good enough to secure a spot on the front row, ahead of the B-Max Nissan of Frederic Makoweicki and Kohei Hirate which topped practice.
Nakajima and his #36 TOM'S teammate Yuhi Sekiguchi slipped to fourth in the final classification, ahead of the sister #37 TOM'S car of 2017 champions Nick Cassidy and Ryo Hirakawa and the Kondo Nissan of Jann Mardenborough and Mitsunori Takaboshi.
Button's best Q2 effort was up 0.476s off the pace, as Honda fell behind both Lexus and Nissan in qualifying for the only overseas round of the season.
Only two Hondas made it to the second leg of qualifying, with the other NSX-GT operated by ARTA and driven by Tomoki Nojiri and Takuya Izawa. ending up just behind in eighth.
Impul and NISMO made it an all-Nissan fifth row, with James Rossiter and Daiki Sasaki beating the fully factory-entered car of Ronnie Quintarelli and Tsugio Matsuda by less than a tenth of a second.
The championship-leading Cerumo Lexus, saddled with ballast equivalent to 53 kg, will start on the back of the grid, after ending up 1.3s off the pace in qualifying.