A slow-starting Perez hit an early setback after being caught up in a Turn 1 collision with Mercedes' Lewis Hamilton, with prompted a pitstop for a new front wing.
After being handed a five-second penalty for overtaking Fernando Alonso ahead of his safety car stop, Perez then damaged another front wing - and collected another penalty - for ramming Haas' Kevin Magnussen into the Turn 11 hairpin.
While his car was too damaged to continue at pace, Perez eventually returned from his pitbox so he could serve his second five-second time penalty, thereby avoiding it being converted into a grid penalty for the next race in Qatar.
Horner said avoiding a penalty hangover was the only positive from Perez's disastrous Suzuka weekend, adding that the Mexican was unlucky to get caught up in the Turn 1 melee.
"It got off to a bad start. He got sort of pinballed on the way down to Turn 1, that was unlucky for him," Horner replied when asked by Autosport to explain how Perez' race spiralled out of control.
"He then had damage with Lewis [Hamilton] and broke the front wing. He then passed Fernando on the way in under the safety car, picked up another penalty.
"He goes out a little bit too optimistic, probably out of frustration trying to pass Magnussen...another front wing and the steering damage.
"So, the only decent thing we managed to get out of today was not carrying a penalty through into the next race in Qatar."
Source: Autosport