The occupants of the #36 Toyota GR Supra came through from sixth on the grid to beat the pole-sitting Team Kunimitsu Honda NSX-GT of Naoki Yamamoto and Tadasuke Makino by 28 seconds in the 450km race, which ran completely caution-free.
Rounding out the podium was the Real Racing Honda of Nobuharu Matsushita and Koudai Tsukakoshi after both the Kondo Racing Nissan and #8 ARTA Honda hit late dramas.
Poleman Makino led the early stages in the Kunimitsu Honda, but was kept honest throughout the opening stint by fellow NSX driver Nirei Fukuzumi in the #16 ARTA car.
Tsuboi meanwhile held position in the opening laps but was soon climbing the order, pulling off a double pass on the second ARTA car of Tomoki Nojiri and the struggling #19 Racing Project Bandoh of Yuji Kunimoto to grab fourth.
On lap 20, Tsuboi passed Sasaki’s Kondo Nissan to move up to third, and had caught up to the two leading Hondas by the time the first round of GT500 stops began.
At the start of lap 31, Tsuboi picked off Fukuzumi in the ARTA Honda for second, with both Makino and Fukuzumi coming in for their first of two mandatory pitstops that lap.
Tsuboi pitted next time round, managing to jump the Kunimitsu Honda in the process, with a shorter stop promoting the #8 Honda of Nojiri to second once all cars had pitted.
Source: Autosport