Yamashita trailed home 17th on Sunday in by far his worst outing of the season, ending a run of points-scoring finishes dating back to his third-place result at the same track in April.
His team-mate Kazuto Kotaka fared little better, making it as far as 14th from the back of the grid.
Kondo dropped from fourth to sixth in the teams’ standings at Fuji as rivals Dandelion Racing and Nakajima Racing notably took a big step forward.
Despite his strong start to the season, Yamashita admitted that Kondo is still struggling to get fully on top of this year's new SF23 package and that the events of Fuji showed how the team has slipped down the pecking order.
“We don’t really know why we are struggling,” Yamashita told Motorsport.com. “Even this weekend, until FP2, the pace wasn’t bad. But in the race we were suddenly slow.
“We don’t have a deep understanding of the car yet. We still don’t understand why the car behaves in a certain way. It feels like we’ve not made much progress as a team.
“Qualifying wasn’t bad, I was the second-best Toyota runner [in Q2], but our speed in the race was terrible.”
Yamashita had started eighth but lost ground at the start, also making contact with Inging driver Sho Tsuboi at the first corner, but he believes this not cause any damage to his Kondo car that would explain his poor pace.
“I don’t think that had so much of an effect,” Yamashita said of his contact with Tsuboi. “It was only a small touch.
“I got off to a bad start, I lost about three positions off the line. And then after that, at the hairpin, I wasn’t able to turn properly and I went off on my own. I lost more places there and I was basically last at this point.
“Then after that the car didn’t feel right, the pace was poor, and it was really just about getting to the end.”
Kotaka has finished in the points twice in six races so far, peaking with a best finish of seventh at Suzuka, but the Fuji race marked the first occasion on which he has finished ahead of Yamashita.
After qualifying at the very back of the grid, the reigning Super Formula Lights champion reported that adjusting his car to combat the understeer he had been experiencing in last month's test had backfired.
“We changed the set-up a lot from qualifying and I had the impression the car was better, but the pace was worse than I expected in the race,” said Kotaka, who topped Sunday morning's second practice session.
“But compared to qualifying, I think the car was good enough for about 10th, so I want to work with the engineers to improve further for the next race at Motegi.”
