Yamamoto and his partner in the Team Kunimitsu Honda NSX-GT, Tadasuke Makino, came home second behind the victorious Nissan crew of Ronnie Quintarelli and Tsugio Matsuda in Sunday's race, having failed to finish higher than fifth in the two prior races at Fuji.
It came after an impressive recovery drive from eighth on the grid, with Makino progressing all the way to second in a rapid stint before pitting to hand over to Yamamoto.
However, Yamamoto admitted to some disappointment that he couldn't threaten the Nissan of Matsuda for the lead during his stint.
Naoki Yamamoto, Tadasuke Makino on the podium (#100 RAYBRIG NSX-GT)
Makino admitted the Michelins of the winning Nissan GT-R were better suited to Suzuka's hot conditions than his Honda's Bridgestones, but was satisfied to make so much progress after struggling in dirty air in the two Fuji races.
"After qualifying we did a big change on car set-up and it’s working well," he told Motorsport.com. "We weren’t struggling with tyre pick-up this time, I think that’s why I was consistent and quick at the end of my stint.
"The #23 car was quite quick, I thought we would catch up but it seemed the Michelin was more suited to the conditions. Anyway, P2 is not a bad result, [especially] after we struggled so much with race pace in the first two rounds."
Yamamoto and Makino now sit third in the championship, 15 points down on the #36 TOM'S Toyota crew of Sacha Fenestraz and Yuhi Sekiguchi, who finished third at Suzuka.
For the next race at Motegi, Yamamoto and Makino will be carrying a 52kg handicap, including the 'stage one' fuel restrictor that both TOM'S cars had to use at Suzuka.
"Winning is important, but more important is to be in the title battle by the time of the final race," said Yamamoto. "Although there is a gap to the top car, SUPER GT has a weight handicap so it is not easy for the leader to escape.
"So to that end, I want to work hard to win the championship. I think it was a good race."
Makino added: "In the next round we have quite a lot of weight, but the #36 car has been consistent [despite carrying a lot of ballast], so we should improve more.
"I don’t know what will happen at Motegi because we haven’t driven the front-engined NSX there. We’ll see what we can do, but qualifying better will be very important."
#100 RAYBRIG NSX-GT