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, with a similar margin over the third-placed NISMO Nissan of Tsugio Matsuda, when the conditions started to deteriorate.
With a seven-point gap in hand over the NDDP Nissan crew, Miyata only needed to bring the car home in second to guarantee himself and Tsuboi the title, and closed in on Takaboshi as the leaders started circulating up to 15s a lap off the pace.
The gap was down to around five seconds when Takaboshi made a crucial error on lap 59 of 63 and spun his Nissan at the Turn 8 right-hander, ending up beached in the gravel.
That allowed Miyata to take the lead, which he held to the chequered flag by five seconds over the 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.
Completing the podium was the #17 Real Racing Honda NSX-GT of Koudai Tsukakoshi and Nobuharu Matsushita, which was among a minority of cars to change to wet tyres in the closing stages but lacked the pace to catch the leading two cars.
Tsukakoshi passed Matsuda in a thrilling fight for third on lap 53, but surrendered the place by pitting on lap 57 to change to wets, and while the gamble looked like it could pay off initially, the rain wasn't heavy enough to allow Tsukakoshi to close the gap.
He and Matsushita finally fell 16s short of delivering Honda a farewell win for the NSX-GT.
Fourth place went to outgoing champions Bertrand Baguette and Kazuki Hiramine in the Impul Nissan, while ARTA Honda duo Tomoki Nojiri and Toshiki Oyu wrapped a tumultuous season with a smooth run to fifth in the #8 NSX-GT.
The sister #16 ARTA car of Nirei Fukuzumi and Hiroki Otsu, who entered the race with slim title aspirations, ended up 12th after also changing to wet tyres in the latter stages. That meant they were beaten to third in the championship by Quintarelli and Matsuda by three points.
Rookie Racing Toyota duo Kenta Yamashita and Kazuya Oshima finished sixth despite Oshima being turned around by the Kunimitsu Honda of Iori Kimura in an early battle for fifth position.
Kimura was handed a drive-through penalty for the offence, limiting he and Tadasuke Makino to the final points position in 10th.
Yuji Tachikawa wrapped up his illustrious GT500 career in 11th place alongside Cerumo Toyota team-mate Hiroaki Ishiura, while Chiyo and Takaboshi were finally classified 13th.
GT300 title honours went to Saitama Toyopet Toyota pair Hiroki Yoshida and Kohta Kawaai, who needed only a single point to wrap up the title and finished seventh in the treacherous conditions.
Victory in the final race went to JLOC Lamborghini duo Takashi Kogure and Yuya Motojima, who beat LEON Racing Mercedes pair Naoya Gamou and Takuro Shinohara by seven seconds.
