From pole position, Yamamoto and Makino finished a distant second in the Golden Week race, ending up some 28 seconds down on the #36 TOM'S Toyota GR Supra of Sho Tsuboi and Ritomo Miyata.
Makino was at the wheel of the Kunimitsu car for the opening two stints of the 450km race, completing almost two thirds of the race before pitting to hand over to Yamamoto on lap 63 of 100.
The two-time GT500 champion, who only barely scraped through Q1 in eighth before Makino took pole in Q2 with a time eight tenths faster, felt that his team-mate deserved the credit for the team's result.
"Simply, it was all thanks to Makino," said Yamamoto post-race. "I was just a bit lacklustre.
"I didn’t think Makino could go that fast [in Q2]. That was what made the difference [from Q1]."
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Polesitter Makino held the advantage throughout the opening stint, but by the time he had made his first stop on lap 31, he was already under attack from Tsuboi in the TOM'S car, and a faster pitstop and outlap for the #36 crew put Tsuboi out front for the second stint.
After taking over for the final stint, Yamamoto was being reeled in by the Kondo Racing Nissan of Kohei Hirate, only to be saved by Hirate getting tangled up with GT300 traffic with five laps to go.
The Kunimitsu squad was also given further breathing space when the #16 ARTA Honda picked up a costly drive-through penalty for an infraction at its first stop, prior to which Makino was battling with Nirei Fukuzumi for the lead.
"If we look at the pace overall, we have to be happy with second," reflected Yamamoto. "If we look at the laptimes and the fastest laps, we definitely didn’t really deserve to be second.
"Makino did a great job in his stints and kept us at the front of the field, because if we had slipped into the chasing pack, we wouldn't have had the pace to recover.
"His performance in both qualifying and the race was amazing, so the fact we were able to finish second was all down to his hard work."
Honda SUPER GT project leader Masahiro Saiki said that tyre pick-up was a major factor behind the Kunimitsu NSX-GT being unable to keep up the pace against the winning TOM'S Toyota.
"Although we took pole position, in the race there was a performance deficit due to the set-up and tyre matching, and in the end we couldn't compete with the #36 car," commented Saiki.
"In clean air, the pace was about the same as the #36 car, but after hitting GT300 traffic, due to tyre pick-up, it took time to get back to our previous pace and we gradually fell further behind.
"We have another race at Fuji this season [Round 4 in August], so we'll do our best to have a better race then."
