A slow-starting Perez hit an early setback after being caught up in a Turn 1 collision with Mercedes' Lewis Hamilton which 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 Motorsport.com to explain how Perez's 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."
Perez explained that his first hit with Hamilton caused more damage to his RB19 beyond the broken front wing.
He believes that yet to be diagnosed additional damage is what caused his second smash with Magnussen, although he still took responsibility for barging into the Dane's Haas.
"I had a horrible start and basically going into Turn 1, I was just a passenger," he said.
"I had Sainz on my right, Lewis on the left, and they just took the whole front wing endplate off.
"We changed the front wing and I still had no front end, so I think there were a lot more things damaged on the car.
"I was struggling quite a lot on the braking with the front end. I just wouldn't stop in time and it was my mistake, obviously."
