Not for the first time this year, Perez struggled to get going in Japan after having issues to get the RB19 balanced to his liking in Friday practice.
Overnight work did little to improve matters as he qualified fifth, some seven tenths behind his dominant team-mate Max Verstappen.
Perez's Suzuka race quickly spiralled out of control after he made contact with Mercedes' Lewis Hamilton at the start and later speared into Haas' Kevin Magnussen.
He received a five-second penalty for the latter incident, and another one for overtaking Fernando Alonso under the safety car as he came in for a new front wing.
Team principal Horner admitted that Perez sitting out his second time penalty in Japan instead of carrying it over to the next race in Qatar was the only positive from the Mexican's weekend.
But Perez's confidence issues through high-speed corners, of which Suzuka has many, remain at the heart of his massive performance gap with Verstappen.
"This is a big confidence circuit and where Sergio was struggling was mainly in the high-speed corners compared to Max," Horner explained.
"You could tell Max the confidence that he had, the speed that he was able to carry through the high-speed stuff was mind boggling."
When asked if the performance gap between Perez and Verstappen was problematic for when Red Bull faces a stiffer challenge by rival teams, Horner continued to point to Verstappen's dominant form as the main factor between their lap time difference.
"He's still second in the world championship and I think he's finished second to Max six times so far," he added.
"So, had Max not been there it would have been another six races on top of the two he'd already won.
"Max is absolutely at the top of the game. He's the best driver in Formula 1 at this point in time and I think everything has to come together; car, driver, team in total harmony."
