While his team-mate Jenson Button could only qualify 14th in McLaren's revised car, Perez made it to the pole shootout, taking seventh place in Q2.
The Mexican was 1.3 seconds off the pace in Q3 and started ninth.
He reckoned he would have been better off saving the tyre life used on those laps, having struggled to keep his Pirellis alive on a four-stop strategy on race day, when ninth was again his limit.
"I think we are paying for doing laps in Q3," Perez said.
"We gained positions, but in the end, towards the end of the race we lost quite a lot.
"Doing a few laps in Q3 really affected us today."
Perez was ultimately beaten by Button, who got through the race on three pitstops.
The Briton achieved that result despite dropping to 17th with what he admitted was a "shocking" start.
But though he salvaged points, Button fears McLaren stood still in Spain even with its upgrades.
"I don't know if we've improved, it's hard to say," he said.
"In Monaco hopefully we'll make another step forward and we can keep progressing.
"It's tough at the moment, but we're making the best of it.
"It's a bit embarrassing driving so far back but we're doing the best we can."
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