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.
Source: Autosport