Yamamoto and Makino matched their best finish of the season aboard the #100 Team Kunimitsu NSX-GT on Sunday, also achieving the minimum result needed to stay in contention for this year's crown.
But the pair had no answer to the pace of fellow Honda squad Real Racing, which took a dominant win with Koudai Tsukakoshi and Nobuharu Matsushita.
The Kunimitsu car of Makino ran ahead of Matsushita in the Real car throughout the opening stint, holding second until Makino pitted on lap 22 of 65 to hand over the reins to Yamamoto, but faster pitwork allowed Tsukakoshi to exit the pits in front and take a net lead he would hold to the finish.
Yamamoto admitted he soon realised that he would have to give up on chasing Tsukakoshi and focus on defending second from Kohei Hirate's Kondo Nissan once he started running out of grip.
"At a certain point the tyres wore out and I had no grip," Yamamoto told Motorsport.com's Japanese edition. "With about 20 laps to go, I thought it would be tough [to keep hold of second].
"This season we’ve had a lot of races where we’ve not been able to keep the tyres alive, so that’s been one of our biggest problems this year and a factor in why we haven’t had the results we wanted.
"We’ve been working hard to resolve this issue, so it’s frustrating that it’s happened again."
Second at Autopolis keeps Yamamoto and Makino within 17 points of the championship lead with 21 left on the table in the final round at Motegi next month; had Yamamoto slipped to third, they would have faced an insurmountable deficit to the points-leading NDDP Racing Nissan crew.
Last year, Yamamoto led the drivers' standings heading into the season finale at Fuji, only for his hopes of becoming SUPER GT's first solo champion since 2000 to be wrecked by a collision with the ARTA Honda NSX GT3 of Ren Sato.
But the two-time GT500 champion said his desire to simply finish the season with at least one win was more significant than any feelings of revenge.
"It feels like, ‘was last year’s final race really only one year ago?’" said Yamamoto. "It’s not like I have no desire for ‘revenge’ at all, but it’s already in the past and it’s not like I’m racing for that reason.
"More than that, we haven’t won a race all year, so I want to show our strength in the final race. I want to solve the problems we’ve faced all year and end the season with a win.
"It would be great if that also meant we became champions, but quite simply, I just want to win again."
- Stream every qualifying session and race of the 2022 SUPER GT season only on Motorsport.tv.
