Katsumasa Chiyo and Mitsunori Takaboshi looked on course for a commanding victory from pole in the #3 NDDP Nissan Z for much of the race, but the arrival of rain in the closing stages opened the door for a late twist in the title battle.
Miyata was running in second, around 10 seconds behind Takaboshi, when the conditions started to deteriorate, and in a position to win the championship if the positions didn't change.
But once the rain started to fall harder, Miyata started to close the gap to around five seconds when Takaboshi made a crucial error and spun his Nissan at the Turn 8 right-hander.
That allowed Miyata to take the lead, which he held to the chequered flag by five seconds over the sister NISMO Nissan of Tsugio Matsuda and Ronnie Quintarelli, bagging a first title for himself and a second for Tsuboi.
The third win of the season meant that the #36 TOM'S crew finished 26 points clear of Chiyo and Takaboshi in the final championship standings.
Miyata became only the fifth driver in history to claim a double of titles in Super Formula and Super GT in the same year.
Source: Autosport