With dark clouds overhead and some rain in the buildup to Q2, Espargaro snuck into the lead with seconds to spare, ahead of KTM's Australian Miller in second and Pramac Racing's Martin in third.
Spaniard Espargaro will count himself lucky to have taken pole in front of his home crowd, having narrowly avoided hitting a cat that strayed onto the track earlier in the day before taking a fall during practice.
"It's been a crazy morning," Espargaro said. "Unfortunately I had a crash. When I saw the rain I was a bit angry and disappointed, but I'm happy because I controlled everything until the last lap and really pushed."
Brad Binder and Francesco Bagnaia will line up fourth and fifth on Sunday after coming through a hotly contested Q1.
In Q1, the pair of Binder and Bagnaia beat championship leader Marco Bezzecchi and Fabio Quartararo - who took pole in Jerez for three straight years between 2019-2021.
Ducati's Enea Bastianini, who suffered a right shoulder blade fracture in the MotoGP season-opener in Portugal last month, was expected to return to competition this weekend but withdrew in pain.
"He said it is too painful after a couple of laps, it is too hard to ride. We don't want to take too many risks, so he decided to stop," Ducati team manager Davide Tardozzi said.
Honda's six-times MotoGP champion Marc Marquez is also ruled out for the weekend and was replaced by Iker Lecuona.
