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Nakajima Racing’s Takuya Izawa was the first driver to set a lap time in Q3, clocking the Suzuka circuit in 1m37.935s.
Honda protege Nirei Fukuzumi then posted a 1m36.991s flyer to take over the top spot, only for 2013 champion Yamamoto to deny him a debut pole by going 0.080s quicker in the sister Honda.
Dandelion’s Takuya Izawa ended up third with a late lap of his own, a further 0.049s behind Fukuzumi.
Izawa’s previous lap was good enough to put him fourth on the grid, ahead of the Real Racing car of Koudai Tsukakoshi.
Hiroaki Ishiura, who beat Pierre Gasly to the 2017 title, was Toyota’s top qualifier in sixth, albeit 1.431s slower than Yamamoto’s pole time of 1m36.911s.
Former F1 driver Kazuki Nakajima, also in a Toyota-powered car, was another tenth behind in seventh, while defending Super GT champion Ryo Hirakawa was the last of the Q3 qualifiers in eighth.
Hirakawa didn’t set a time in the final part of qualifying session after suffering a huge crash in the dying minutes of Q2.
The incident brought out a red flag, and even though race control extended the session by three minutes to give each driver enough time to set one flying lap, Hirakawa’s previous time was good enough to progress to Q3.
Former champion Yuji Kunimoto was the first driver to fail to make the Q3 cut, missing out on a top-eight grid spot by less than a tenth of a second.
He will be joined on the fifth row by former F1 driver Kamui Kobayashi, who qualified 0.007s behind in 10th.
Nobuharu Matshushita, who returns to Japan this season after three seasons in F2/GP2, could do no better than 12th despite topping Q1 on his debut.
Reigning Formula V8 3.5 champion Pietro Fittipaldi propped up the timesheets in 19th place, qualifying six tenths behind his Team LeMans teammate Kazuya Oshima.
|8||Ryo Hirakawa||Impul/Toyota||No Time|
|9||Yuji Kunimoto||Inging/Toyota||(Q2) 1'37.933|
|15||Nick Cassidy||Kondo/Toyota||(Q1) 1'38.703|
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