The 21-year-old Spaniard knocked home hero Scott Redding off the top spot with eight minutes to go and then resisted a late charge by Andrea Iannone to hold on to pole.
Behind the Pons Kalex rider, Iannone was 0.385 seconds slower on his Speed Master Speed Up, while Marc VDS Kalex man Redding - his last lap ruined when he came across a slowing Thomas Luthi at Chapel - fell to third by the end.
Bradley Smith made it two British riders inside the top four on his Tech 3, while Marc Marquez (Monlau Suter) and Claudio Corti (Italtrans Kalex) completed the top six.
Championship leader Luthi will start seventh on his Paddock Suter.
Max Neukirchner, Julian Simon and Esteve Rabat all crashed.