Celebrating his 26th birthday, Yamaha rider Lorenzo, who was also fastest in Friday practice, set a best time of one minute 38.67 seconds at the sun-drenched Jerez circuit, with Pedrosa clocking 1:38.92 and Honda team mate Marquez 1:38.971.
Cal Crutchlow of Britain was fourth fastest on his Yamaha ahead of the third race of the season and the first in Europe with a time of 1:39.26 followed by Italian former world champion Valentino Rossi, also on a Yamaha, in 1:39.30.
Lorenzo's job was made easier after Pedrosa, Marquez, Crutchlow and Rossi all suffered crashes during an incident-packed afternoon.
Lorenzo and rookie Marquez top the championship standings on 41 points after two races, with Pedrosa on 33, Rossi on 30 and Crutchlow on 24.
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