Impul driver Hirakawa made a strong getaway from pole as Yamashita vaulted into second from third on the grid ahead of rookie teammate Fenestraz.
And that was how the top three order remained throughout the 35-lap race, which featured no mandatory pitstop - although some drivers further down the order did change tyres - and very few on-track position changes after the opening lap.
Hirakawa never opened up a lead of more than 1.5s throughout the race over Yamashita, who in turn was rarely able to get closer than a second to the leader until the final laps.
Despite Yamashita's late charge, Hirakawa hung on by 0.610s for his second win in Super Formula, which came 12 months on from his maiden triumph at Motegi last year.
Fenestraz completed the podium behind Kondo Racing teammate Yamashita, resisting race-long pressure from TOM'S driver Kazuki Nakajima.
Best of the Honda-powered drivers at the finish was Nirei Fukuzumi in fifth, although the Dandelion Racing man gained the place after contact with Yuhi Sekiguchi.
Hirakawa's Impul teammate Sekiguchi settled into fifth place in the early laps but couldn't keep up the pace of the top four, and a train of cars led by Kamui Kobayashi formed behind him.
Fukuzumi finally cleared Kobayashi's KCMG car for sixth place on lap 19 and two laps later he was on the tail of Sekiguchi, but as he tried to dive up the inside heading into the long Turn 6 right-hander the two cars touched, Sekiguchi spearing off into the gravel.
Escaping damage in the incident, Fukuzumi was able to come home 11s adrift of Hirakawa.
Reigning champion Nick Cassidy (TOM'S) made up five places from his grid slot to finish sixth, helped by Kobayashi sustaining a puncture after making contact with Naoki Yamamoto (Dandelion), who had to pit to replace a damaged front wing at the end of lap 20.
Completing the points-scorers were Tomoki Nojiri (Mugen), Hiroaki Ishiura (Inging), Tadasuke Makino (Nakajima Racing) and Kazuya Oshima (Inging).
Juri Vips' replacement Ukyo Sasahara (Mugen) was the best of the drivers to change tyres in 11th place, and although he was two seconds faster on fresher rubber he couldn't find a way past Oshima in the closing laps.
Tatiana Calderon (Drago Corse) likewise changed tyres and finished 12th, fiercely defending her position from the similarly one-stopping Yamamoto on the final lap.
Toshiki Oyu (Nakajima Racing) ended up four laps down in 15th, behind Kobayashi, after slowing with mechanical trouble on the first lap exiting the hairpin and pitting.
|1||20||Ryo Hirakawa||ITOCHU ENEX TEAM IMPUL||35|
|2||3||Kenta Yamashita||Kondo Racing||35||0.610|
|3||4||Sacha Fenestraz||Kondo Racing||35||3.331|
|4||36||Kazuki Nakajima||Vantelin Team TOM'S||35||7.556|
|5||6||Nirei Fukuzumi||DoCoMo Team Dandelion Racing||35||11.179|
|6||1||Nick Cassidy||Vantelin Team TOM'S||35||19.929|
|7||16||Tomoki Nojiri||Team Mugen||35||26.930|
|8||38||Hiroaki Ishiura||JMS P.mu/cerumo-INGING||35||27.854|
|9||64||Tadasuke Makino||TCS Nakajima Racing||35||38.030|
|10||14||Kazuya Oshima||ROOKIE Racing||35||39.497|
|11||15||Ukyo Sasahara||Team Mugen||35||40.664|
|12||12||Tatiana Calderon||ThreeBond Drago CORSE||35||1'02.537|
|13||5||Naoki Yamamoto||DoCoMo Team Dandelion Racing||35||1'02.679|
|14||7||Kamui Kobayashi||carrozzeria Team KCMG||35||1'03.270|
|15||65||Toshiki Oyu||TCS Nakajima Racing||31||4 Laps|
|16||18||Yuji Kunimoto||carrozzeria Team KCMG||22||13 Laps|
|17||19||Yuhi Sekiguchi||ITOCHU ENEX TEAM IMPUL||20||15 Laps|
|18||39||Sho Tsuboi||JMS P.mu/cerumo-INGING||0|
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