While times had been extremely close on Tuesday and Wednesday, Pedrosa moved clear on day three.
The Honda rider set the best time of the week with a 2m00.100s lap, 0.329 seconds clear of Yamaha rival Jorge Lorenzo.
Valentino Rossi was only 0.113s behind Lorenzo on the second Yamaha in third place. The Italian felt on Wednesday that he was already up to speed and would have matched his team-mate but for a mistake on his best lap.
Rookie Marc Marquez had his first blip when he crashed at the final corner during the morning. He was unhurt and rejoined later to secure fourth.
Cal Crutchlow was best of the rest once again on the Tech 3 Yamaha, with his new team-mate Bradley Smith eighth behind Stefan Bradl and Alvaro Bautista.
The works Ducatis of Nicky Hayden and Andrea Dovizioso fell back to being two seconds off the pace in ninth and 10th, while Pramac's Andrea Iannone was outpaced by CRT leader Aleix Espargaro's Aprilia.
Iannone was the only Pramac rider in action as Ben Spies chose to skip the final day to rest his still-recovering shoulder.
One of the best performances of the test came from Paul Bird's rookie rider Michael Laverty, who was second-fastest among the CRTs, only 0.2s behind Espargaro.
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