Hirakawa had topped both Saturday's first practice session and the 20-minute session that preceded qualifying, and set an impressive time of 1m31.096s in Q2 to beat the pole record established by Alex Palou at Motegi last year.
In the seven-minute Q3 pole shootout, Hirakawa made a small improvement to log a 1m31.096s and put himself 0.313s clear of Kondo Racing's Fenestraz, who was slightly slower in Q3 than he had been in Q2.
Fenestraz's teammate Kenta Yamashita was third-fastest, a further tenth behind and just ahead of the only Honda runner in Q3, Nakajima Racing rookie Toshiki Oyu.
Kazuki Nakajima was fifth for TOM'S, while the Q3 order was completed by Hiroaki Ishiura (Inging), Hirakawa's Impul teammate Yuhi Sekiguchi and Kamui Kobayashi (KCMG).
Missing out on the pole shootout by just 0.016s was Nirei Fukuzumi (Dandelion), who went three tenths slower in Q2 than he managed in Q1.
He'll start ninth ahead of Yuji Kunimoto (KCMG) and reigning champion Nick Cassidy (TOM'S), who was a little under a tenth shy of the cut-off to make into Q3.
Dandelion lost both cars in Q2 as Naoki Yamamoto was slowest of all, meaning the two-time champion starts 14th behind debutant Ukyo Sasahara (Mugen).
Tadasuke Makino was the biggest name to be eliminated in Q1, the Nakajima Racing ended up eighth in his group and the wrong side of the Q2 cut-off and leaving him down in 15th on the grid for this afternoon's race.
Cleared to take part in qualifying following his bout of dehydration on Saturday, Teppei Natori was 18th for B-Max Racing ahead of fellow rookie Tatiana Calderon (Drago Corse).
Results to follow