Dandelion Racing driver Fukuzumi again prevailed during a late fresh-tyre shootout in the 130-minute Wednesday afternoon session, setting a best time of 1m21.207s.
That was enough to beat nearest challenger Ryo Hirakawa (Impul) by 0.241s, although it fell short of his fastest time in the morning session and Hirakawa's Tuesday benchmark.
The session was disrupted by no fewer than three red flags, the first of which was triggered by TOM'S man Kazuki Nakajima spinning off at Turn 4.
Not long after action resumed, Kamui Kobayashi's KCMG car sustained a left-rear puncture, causing him to go off at the same corner, while his teammate Yuji Kunimoto suffered a similar problem later in the session at Turn 9, causing another stoppage.
Red Bull junior Juri Vips (Mugen) had been leading the way on a 1m21.819s before the final stoppage, but this was surpassed by Sacha Fenestraz (Kondo Racing) just after the 90-minute mark as the Frenchman posted a 1m21.782s and then a 1m21.642s.
That was the time to beat heading into the closing minutes, when Fukuzumi went some four tenths faster to top the session for Honda.
Fenestraz's earlier time was good enough for third, followed by Dandelion's 2018 champion Naoki Yamamoto in fourth and the second Impul car of Yuhi Sekiguchi in fifth.
Toshiki Oyu (Nakajima Racing) rounded out an impressive two days in sixth ahead of Vips and another rookie, B-Max/Motopark driver Sergio Sette Camara.
Kobayashi and Nakajima ended up 10th and 12th respectively after their earlier troubles, sandwiched by reigning champion Nick Cassidy (TOM'S).
Drago Corse newcomer Tatiana Calderon concluded the test at the bottom of the order, not improving on her best time from the morning session.
Sergio Sette Camara