Britain's Cal Crutchlow, on a non-works LCR Honda, denied Spain a trio of home riders on the front row for Sunday's race with Yamaha's Maverick Vinales fourth.
The pole, in a time of one minute 38.249 seconds, was Pedrosa's first in 18 months - since Malaysia in October 2015 - and 29th of his career.
He beat triple champion Marquez by 0.049 of a second, with Sunday's race the first of four in Spain this season.
Yamaha's Italian great Valentino Rossi, leading the championship at the age of 38, starts seventh.
(Reporting by Alan Baldwin, editing by Ed Osmond)
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