The Mexican suffered wing damage on the first lap after being sandwiched between Carlos Sainz and Lewis Hamilton, before colliding with Kevin Magnussen later in the race as he looked to climb the leaderboard.
Perez was given two five-second penalties: one for the incident with Haas driver Magnussen and another after overtaking Fernando Alonso under yellow flag conditions.
“It was a shocker of a race for him today,” Horner told Sky F1.
“It got off to a bad start where he sort of got concertinaed on the rundown to turn 1, he picked up some front wing damage, then we needed to change the front wing.
“He overtook Fernando on the way into the pit lane, then picked up a penalty and then came out and of course, then he dive-bombed one of the Haas’ and so it was just one of those weekends.”
However, having originally retired on lap 15, Perez befuddlingly re-entered the race 26 laps later in order to serve his time penalty, meaning it won’t carry over to a grid drop for the next race in Qatar.
“The only good thing was were able to serve the penalty here,” Horner added. “So he leaves it here in Japan.”
Verstappen can now secure his third world title in the sprint race in Qatar, with Perez trailing his team-mate by 177 points in the world championship. Perez’s lead to Lewis Hamilton in third has also been cut to 33 points.
Perez has a contract with Red Bull until the end of the 2024 season, but his inconsistent form this season has prompted the likes of Lando Norris, Daniel Ricciardo and even Liam Lawson to be linked with the second Red Bull seat next year.