Reigning champion Yamamoto ended up just 0.024s behind his teammate in second, with Nakajima Racing’s Palou a further 0.480s adrift in third.
Autopolis winner Sekiguchi was classified fourth as the top Toyota-powered driver, with TOM’S Nick Cassidy just behind in fifth.
Mugen driver Tomoki Tsukakoshi was classified sixth, while Tsukakoshi slipped down to seventh in the final order amid the late flurry of laps.
Yamashita finished eighth ahead of Hirakawa, while the top 10 was completed by B-Max/Motopark driver Lucas Auer.
Harrison Newey and Dan Ticktum languished down in 14th and 15th respectively, separated by a tenth of a second, while Artem Markelov propped up the timesheets in 20th position.
Reigning Japanese F3 champion Sho Tsuboi brought out the sole red flag of the session when he crashed at the SP Out left-hander. He ended up 18th in the classifications after failing to return to the track following his crash.