Impul driver Hirakawa again ended up fastest amid a late flurry of improvements as the majority of the field equipped new tyres in the final 10 minutes of the two-hour session.
Prior to that, Hirakawa had set the pace on a 1m21.103s, having become the first driver to improve on his benchmark from the morning.
Nakajima Racing rookie Toshiki Oyu and Dandelion's Nirei Fukuzumi both briefly hit the top of the times with the first sub 1m21s laps of the day, but Hirakawa was able to beat them both with his final time of 1m20.677s - just 0.017s clear of Fukuzumi.
The second Dandelion car of Naoki Yamamoto was fourth-fastest, just 0.007s slower than Oyu, while Tomoki Nojiri made it four Honda-powered drivers in the top five.
Nojiri's Mugen teammate Juri Vips enjoyed a stronger afternoon session, the Red Bull junior ending up seventh-fastest behind Kazuki Nakajima (TOM'S).
Completing the top 10 were Tadasuke Makino (Nakajima), Yuhi Sekiguchi (Impul) and Sacha Fenestraz (Kondo Racing).
Kamui Kobayashi was able to return to action in the afternoon having sat out the morning session following his crash, and ended up 12th-fastest in the best of the KCMG cars.
Defending champion Nick Cassidy was among those not to equip new tyres for the final part of the session and concluded the day 17th-fastest, 1.540s off the pace.
New B-Max/Motopark signing Sergio Sette Camara completed only 11 laps in the afternoon after spending the first hour in the garage, ending up 19th, ahead of fellow Super Formula newcomer Tatiana Calderon in the solo Drago Corse car.
The Fuji test will conclude with two more sessions on Wednesday, which have been extended by 10 minutes each to make up for the disrupted start to Tuesday's action.
Sergio Sette Camara