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 pole-winning 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."
Explaining his struggles, Perez said: "I think mainly it was Turn 5.
"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."
Echoing the views of second place starter Carlos Sainz, who predicted that Perez can still secure a 1-2 finish for Red Bull, Horner believes the Mexican can still turn things around in Sunday's race.
"I think it's a matter of just picking him up," he said. "I mean, the points are scored on Sunday.
Source: Autosport