Perez's time of 1:21.848s was three tenths of a second faster than reigning world champion Sebastian Vettel.
Vettel, who topped the morning session, caused the first red flag of the day when his Red Bull RB9 stopped shortly after the pit exit in the final hour of running due to a loose wheel.
It was another disappointing day for Lotus. Despite setting the third fastest lap time, Kimi Raikkonen spent much of the day in the garage as a gearbox problem limited his running to a mere four laps. He emerged with just under two hours remaining.
Lewis Hamilton set the fourth quickest time in the Mercedes W04 and was also the most productive driver, completing 121 laps at the home of the Spanish Grand Prix.
Fernando Alonso had a minor exhaust issue but was fifth, ahead of Williams rookie Valtteri Bottas in the FW35.
The only other red flag on the second day of running was caused by the Marussia of Max Chilton, who stopped during the final five minutes between Turns 12 and 13 during a planned fuel test.
A number of driver changes will take place for tomorrow's running, the most documented being the return of Adrian Sutil with Force India.
|1||S. Perez||McLaren MP4-28||1:21.848||97|
|2||S. Vettel||Red Bull RB9||1:22.197||84|
|3||K. Raikkonen||Lotus E21||1:22.697||43|
|4||L. Hamilton||Mercedes W04||1:22.726||121|
|5||F. Alonso||Ferrari F138||1:23.247||76|
|6||V. Bottas||Williams FW35||1:23.561||98|
|7||D. Ricciardo||Toro Rosso STR8||1:23.718||70|
|8||P. di Resta||Force India VJM06||1:23.971||62|
|9||N. Hulkenberg||Sauber C32||1:24.205||88|
|10||M. Chilton||Marussia MR02||1:25.115||67|
|11||C. Pic||Caterham CT03||1:26:243||102|