Spaniard Pedrosa delighted the home fans thronging the circuit in sweltering heat with a blistering time of 1:40.893 on his Honda.
Yamaha pilot Cal Crutchlow of Britain was second fastest, with Pedrosa's compatriot, world champion Jorge Lorenzo, third quickest on another Yamaha.
"It's a difficult circuit, above all when it is so hot," Pedrosa said in an interview with Spanish television broadcaster Cuatro.
"We got a good lap in but even more pleasing is that we have improved in terms of rhythm and that is the most important factor here," added the 27-year-old. "I am happy to have set the record in front of all my fans."
Pedrosa's time beat the previous record of 1:41.186 set by former world champion Casey Stoner of Australia in 2008.
After five races, Pedrosa tops the standings on 103 points, with Lorenzo second on 91 and Pedrosa's team mate, Spanish rookie Marc Marquez, third on 77.
Marquez was sixth quickest on Saturday, behind Alvaro Bautista in fourth and Nicky Hayden in fifth.
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