Having started last in Monaco after a crash in Q1, Perez again had a torrid time in Barcelona, scraping through to Q2 in 15th place and then going off into the gravel at Turn 5 late in Q2.
Although he had time for another run, he struggled to get his tyres in the right window and could only qualify 11th, 10 place behind team-mate Max Verstappen.
"Unfortunately, the off that he had in Q2, I think it just unsettled him a little," Horner told Sky F1.
"And it was one of those days for him. So P11 for him tomorrow leaves him with quite a bit to do."
Horner insisted that Perez can still turn things around in Sunday's race.
"I think it's a matter of just picking him up. I mean, the points are scored on Sunday. It's obviously harder for him starting from that grid position, but he can still have a great race from there.
"We know he's a great racer, and he's just got to get his head down, and hopefully we can come up with a good strategy and make some good progress.
"I think it's going to be fascinating strategy-wise to see who picks what strategy, who picks what tyres for the start of the grand prix.
"And I think that's what will come into play tomorrow it's all going to be about tyre deg, unless of course it's raining."
Perez expects the new circuit layout to make it easier to progress through the field.
"I think mainly it was Turn 5," he said of his difficult session. "Once we lost it, the tyres were too warm, too hot, and I couldn't get them back to a good temperature window, and I just didn't have the grip on my final lap, which was a shame.
"Conditions were tricky. And I ended up losing the car into Turn 5. It was tough, it was pretty tough out there to get everything in the right place."
Horner insisted that there was no difference between the potential of the two RB19s despite Perez struggling more than team-mate pole man Max Verstappen.
"I think the tyres are a crucial factor," said Horner. "We checked all the aero loads after Q1. So the support that we have back in the factory, they were able to look at the analysis between the two cars, are the cars generating the same amount of downforce? And they were like-for-like.
"So we couldn't see anything, any part misbehaving. So obviously, we'll do a big inspection this evening, but I think it was just about getting the tyres in the window, because we know Checo's not that far off. It's just that he didn't get the car working today."
