The Mexican experienced issues to the rear of his McLaren during final practice and the team elected to make several changes to the MP4-28 in compensation.
"It was not the best day for me as we had some problems with the rear of the floor in FP3," said Perez, who qualified only 13th. "We went back to the set-up we ran yesterday and it didn't help.
"It made the car very understeery and I struggled to get the tyres up to temperature."
Perez narrowly made it through to Q2 by one-hundredth of a second before taking 13th, while team-mate Jenson Button lines up ninth.
"I have struggled to match him all weekend," said Perez. "But I hope we can get a better result tomorrow."
Button elected not to set a time in Q3 and has the option of choosing which tyre compound to start the race on.
"We chose not to run and played a bit of cat-and-mouse with Nico Hulkenberg," said Button. "It's not too bad - we're on the clean side.
"I don't know what is going to happen in the race, but I think we have put ourselves in the best position for tomorrow."