The Nakajima Racing driver, who is set to remain with the team for a third season next year, posted a best time of 1m35.613s with around 15 minutes remaining in an extended 2hr10min afternoon session to go fastest.
Kondo Racing's Kenta Yamashita made a last-minute jump up to second with a time just 0.051s shy of Yamamoto's benchmark, while Ryo Hirakawa was third-fastest for Impul.
