Tsuboi and Miyata became the first GT500 crew to win three races in a season since Nissan pair Satoshi Motoyama and Benoit Treluyer back in 2011 on Sunday, as they survived a late rain shower to deliver flagship Toyota squad TOM'S its sixth drivers' title.
Their victory came after NDDP Nissan driver Mitsunori Takaboshi spun off from the lead in the tricky conditions on lap 59 of 63.
For Tsuboi, it marked his second GT500 title following his 2021 success alongside Yuhi Sekiguchi, but on that occasion TOM'S entered the season finale as massive outsiders, overturning a 16-point deficit after Honda driver Naoki Yamamoto was taken out of the race in an incident.
This time, Tsuboi and Miyata turned what had been a seven-point lead heading to Motegi into an overwhelming 26-point advantage in the final championship standings as Takaboshi and Katsumasa Chiyo, their nearest rivals, failed to score.
"Two years ago, we won thanks to other cars hitting problems, and the championship depended on what results the other teams and manufacturers got," said Tsuboi.
"This time, we entered the final round leading the championship and in the position of being chased, rather than being the chasers, so it’s brilliant to get the win and decide the title that way while under such huge pressure.
"It was also the case two years ago when I won the championship, but so much goes on in SUPER GT races, and you just have to hope things don’t go against you.
"Sure enough, when the rain fell and the order started to change, I felt again how difficult it is to win in SUPER GT, but this time we took the title with our own strength, which says it all."
Tsuboi described qualifying third on Saturday as a "huge" step towards being able to win the title, as it put he and Miyata in a strong position to take the second-place finish they needed to win the title regardless of what their rivals did.
The 28-year-old highlighted the value of being able to test at Motegi two months prior to the finale, with the team having struggled at the circuit in the 2022 season finale.
"I think it was very important to do the tyre test here in September," said Tsuboi. "We were able to work out the direction we wanted to go with the tyres and the set-up in advance, so I would say being able to do that test was the biggest factor.
"With those results in hand, we were able to do a lot of things differently to usual. I think this is why we were able to win at a circuit that has been our weak point in the past."
Miyata becomes youngest 'double' champion
Miyata meanwhile earned his first GT500 title in his second year as a TOM'S driver in SUPER GT, adding to the Super Formula crown he took the previous weekend at Suzuka.
It made him only the fifth driver to win the coveted 'double' of Japan's top two categories after Pedro de la Rosa, Motoyama, Richard Lyons and Yamamoto, as well as the youngest ever at 24.
"Last weekend I won the title in Super Formula with the same team, and because many of the team members are the same, the morale inside the team was high and everyone had a strong feeling about wanting to win the GT title as well," said Miyata.
"Now I've become champion in all the major categories in Japan, including F4, F3 [Super Formula Lights], Super Formula and now GT500, so now I can go and compete on the world stage with no reservations."
Miyata is expected to leave SUPER GT next season in favour of a full-time World Endurance Championship drive with the ASP Lexus team in the LMGT3 category.