Hirakawa recorded his best laptime of 1m32.483s in the faster morning session, easily beating the benchmark established by teammate Yuhi Sekiguchi in Friday's pre-event test.
That was enough to end both the one-hour session and the day fastest by 0.119s ahead of Kondo Racing driver Kenta Yamashita.
The second session was topped by Nakajima Racing rookie Toshiki Oyu, whose time of 1m32.703s left him third overall and best of the Honda runners, 0.220s off the pace.
Naoki Yamamoto was second in the afternoon and fourth in the combined timesheets for Dandelion Racing, falling just 0.050s shy of Oyu at the very end of the session.
Kazuki Nakajima was third-fastest for TOM'S in the morning, 0.295s off the pace, and led the afternoon session before being demoted to fourth amid a flurry of improvements.
The Toyota FIA World Endurance Championship driver concluded the day fifth-fastest, ahead of Inging man Hiroaki Ishiura and Tadasuke Makino (Nakajima), who was third in the afternoon.
Another Toyota LMP1 racer, Kamui Kobayashi, was eighth for KCMG, while Nirei Fukuzumi (Dandelion) and Sho Tsuboi (Inging) rounded out the combined top 10 order.
Sacha Fenestraz (Kondo) ended the day 11th overall and best of the non-Japanese contingent ahead of Friday's pace-setter Sekiguchi.
Next up was Ukyo Sasahara, replacing Red Bull junior Juri Vips at Mugen, ending up one place ahead of teammate Tomoki Nojiri in only his second day driving the SF19.
Defending champion Nick Cassidy (TOM'S) ended the day a low-key 15th courtesy of his best time in the morning, while Tatiana Calderon (Drago Corse) was 1.6s off the pace in 19th.
|1||20|| Ryo Hirakawa ||ITOCHU ENEX TEAM IMPUL||1'32.483|
|2||3|| Kenta Yamashita ||Kondo Racing||1'32.602||0.119|
|3||36|| Kazuki Nakajima ||Vantelin Team TOM'S||1'32.778||0.295|
|4||38|| Hiroaki Ishiura ||JMS P.mu/cerumo-INGING||1'32.792||0.309|
|5||7|| Kamui Kobayashi ||carrozzeria Team KCMG||1'32.814||0.331|
|6||39|| Sho Tsuboi ||JMS P.mu/cerumo-INGING||1'32.898||0.415|
|7||5|| Naoki Yamamoto ||DoCoMo Team Dandelion Racing||1'32.973||0.490|
|8||65|| Toshiki Oyu ||TCS Nakajima Racing||1'32.977||0.494|
|9||4|| Sacha Fenestraz ||Kondo Racing||1'32.997||0.514|
|10||19|| Yuhi Sekiguchi ||ITOCHU ENEX TEAM IMPUL||1'33.002||0.519|
|View full results|
|1||65|| Toshiki Oyu ||TCS Nakajima Racing||1'32.703|
|2||5|| Naoki Yamamoto ||DoCoMo Team Dandelion Racing||1'32.753||0.050|
|3||64|| Tadasuke Makino ||TCS Nakajima Racing||1'32.813||0.110|
|4||36|| Kazuki Nakajima ||Vantelin Team TOM'S||1'32.854||0.151|
|5||20|| Ryo Hirakawa ||ITOCHU ENEX TEAM IMPUL||1'32.871||0.168|
|6||6|| Nirei Fukuzumi ||DoCoMo Team Dandelion Racing||1'32.876||0.173|
|7||39|| Sho Tsuboi ||JMS P.mu/cerumo-INGING||1'33.034||0.331|
|8||19|| Yuhi Sekiguchi ||ITOCHU ENEX TEAM IMPUL||1'33.175||0.472|
|9||38|| Hiroaki Ishiura ||JMS P.mu/cerumo-INGING||1'33.213||0.510|
|10||4|| Sacha Fenestraz ||Kondo Racing||1'33.221||0.518|
|View full results|