Having topped Saturday evening's practice session, Honda went into qualifying as the clear favourite with its fleet of new front-engined NSX-GTs.
That status was confirmed in the first segment of qualifying as Nirei Fukuzumi broke the existing GT500 lap record at Fuji with a time of 1m26.433s in the #8 ARTA Honda.
But, come the eight-car pole shootout, Fukuzumi's teammate Tomoki Nojiri was unable to replicate that speed, managing a best lap of 1m26.665s.
In the TOM'S Toyota Supra he shares with Nick Cassidy, Hirakawa posted a 1m26.550s with 30 seconds left on the clock - which while slower than Fukuzumi's Q1 benchmark was good enough to beat Nojiri to pole by 0.115s.
The sister #36 TOM's car driven by GT500 rookie Sacha Fenestraz was third-fastest, also underneath the existing record set by Nissan driver Ronnie Quintarelli last year.
Saturday pacesetter Tadasuke Makino was fourth-fastest in the Kunimitsu Honda, followed by Yuji Tachikawa in the best of the Cerumo-run Supras, the #38 car, and the SARD Supra driven by Yuichi Nakayama.
Nissan managed to get only one car into Q2, the #3 NDDP/B-Max Racing GT-R of Katsumasa Chiyo, who was seventh ahead of the best of the non-Bridgestone runners, the Yokohama-shod Mugen Honda driven by Hideki Mutoh.
The Real Racing Honda was the fastest car to be knocked out in Q1 in the hands of Koudai Tsukakoshi, and will start ninth ahead of the #23 NISMO Nissan, qualified by Quintarelli, and the #14 Cerumo Toyota, driven in Q1 by Sho Tsuboi.
In the GT300 class, Naoya Gamou took pole position at the wheel of the LEON Racing Mercedes-AMG GT3 he shares with Togo Suganami with a best lap of 1m36.236s.
#65 LEON PYRAMID AMG
That was enough to beat Katsuyuki Hiranaka in the Gainer Nissan GT-R NISMO GT3 by just 0.061s, while the practice pace-setting Cars Tokai Dream28 Lotus Evora MC was third-fastest in the hands of Hiroki Katoh, 0.163s off the pace.
Saitama Toyopet's all-new GR Supra GT300 was next up in fourth, followed by the quicker of the two apr-run Toyota Prius PHV GR Sports.
ARTA suffered a difficult start to its title defence as Shinichi Takagi was knocked out in the opening group after choosing wet tyres on a rapidly drying track. He and Toshiki Oyu will therefore down in 22nd place in the #55 Honda NSX GT3.
Results to follow