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 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 of Hirakawa.
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 was Ukyo Sasahara, replacing Red Bull junior Juri Vips at Mugen, in only the Asian F3 champion's second day driving the SF19.
Nick Cassidy (TOM'S) ended the day a low-key 14th courtesy of his best time in the morning, while Tatiana Calderon (Drago Corse) was 1.6s off the pace in 19th.
Results to follow