Yamashita and his teammate aboard the #14 Rookie Toyota GR Supra, Kazuya Oshima, commanded the 82-lap race, with Oshima opening a comfortable lead in his stint from pole before handing off to Yamashita.
However, a late full-course yellow period almost ended up costing the team the win as Yamashita lost a major chunk of time to the chasing Team Kunimitsu Honda NSX-GT of Naoki Yamamoto.
In the end, Yamashita - who had been leading by more than 10 seconds heading into the closing stages - held on by just 1.8s from Yamamoto at the finish.
Post-race, he revealed that contact with the car ahead of him on track after the full-course yellow, the Team LeMans Audi R8 LMS GT3 of Yoshiaki Katayama, almost proved disastrous.
"Oshima was really quick in his stint," said Yamashita. "Before the race I said, ‘I’ll be happy if you can hand over to me with a 10-second advantage’, and in the end he handed over with 17 seconds, so I felt I had no choice but to win.
"I wanted to extend the gap even further, but it was harder than I thought to keep up the pace, I had trouble with the GT300 cars, and then when the Studie BMW went off in front of me, there was a full course yellow, and after that the car in front of me [LeMans Audi] had a half-spin and we made contact, so there were a lot of perilous moments.
"Because the pace was not good, the #100 [Kunimitsu Honda] caught up by a lot, and although we won I was not that happy. That said, we were still able to somehow win and so it was a good start to our championship bid."
Yamashita and Oshima's victory at Okayama marked Rookie Racing's second in SUPER GT as an independent outfit, with their first coming at the same track a year ago.
Oshima, whose Q2 effort on Saturday put the #14 machine on pole, admitted to being surprised at just how much pace the team had over the weekend.
"Since we won last year’s opener, we’ve grown a lot as a team," said Oshima. "So I came to the track thinking we can get a good result, but I was surprised at just how well things went.
"The car was in good condition and the tyres were able to run to the end without dropping off, so I think it’s really thanks to everyone in the team [that we could win].
"Qualifying for the next race [at Fuji] will be tough because of the success weight [42kg], but because the race is longer [450km] I think our chances of a good result will increase.
"There are some things from this race that we need to work on, so I want to improve on those and prepare so that we can fight for consecutive wins."
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