The Spanish rider prevented defending champion Casey Stoner from completing a clean sweep of all three practice sessions by topping the timesheets on his Yamaha in one minute 55.302 seconds.
Stoner (Honda) dropped to third in 1min 55.674secs as Cal Crutchlow (Tech 3 Yamaha) also went faster than him.
The Australian, who was quickest in opening practice on the Losail circuit yesterday, maintained that form in the second session this afternoon, going fastest in 1:55.960.
He just managed to edge out Lorenzo by 0.214 with Italy's Andrea Dovizioso (Yamaha Tech 3) third quickest.
Dovizioso continued that form in the final session this evening as he went fourth quickest.
But Ben Spies (Yamaha), who was fourth in second practice, could only manage 11th in the final session after crashing early on.