Yamamoto was running in eighth place in the #100 Honda NSX-GT at the time of the crash, having just taken over at the wheel from team-mate Tadasuke Makino.
The two-time GT500 champion appeared to lose control exiting the final corner, spearing into the barriers on the left-hand side at the end of lap 39.
Moments later the safety car was deployed, before the red flags followed with 40 laps completed.
Yamamoto was reported to be conscious and able to communicate with the team over the radio. A further update from SUPER GT stated that the 35-year-old was in pain but able to move his arms and legs.
While the reason for the crash remains unclear, the #56 Kondo Racing Nissan GT-R NISMO GT3 was seen carrying some front-right damage, having come into the pit at the time of the safety car being called.
The SARD Toyota GR Supra of Yuhi Sekiguchi led the way at the time of the stoppage ahead of the Impul Nissan Z of Bertrand Baguette, with neither car having made its mandatory pitstop.
Third was the Real Racing Honda of Koudai Tsukakoshi, who held the net lead ahead of the pole-winning ARTA NSX-GT of Toshiki Oyu and the NISMO Nissan of Tsugio Matsuda.
Leading in the GT300 class was the #87 JLOC Lamborghini of Natsu Sakaguchi, who was also yet to pit.
The race was scheduled to be resumed at 15:20 local time.