Pedrosa and Lorenzo work hard for final practice
Pedrosa, Casey Stoner and Lorenzo had been covered by just 0.3s in Friday's only dry session, with all three choosing to skip the wet afternoon practice.
Lorenzo then made a hot start to Saturday's session, beating Pedrosa's Friday time within three laps. The Yamaha star remained on top until Pedrosa took over by 0.158s just before the halfway stage.
That kept Pedrosa, winner of four of the past five races but still 28-points from Lorenzo, in charge to the end. The soft rear tyre was again the preferred choice. Pedrosa's best time was set on lap 6 of 16 and Lorenzo lap 3 of 19.
While Pedrosa and Lorenzo were up front from the start, Stoner - who looked in much better physical shape on Friday relative to his comeback from ankle surgery last weekend at Motegi - appeared to suffer front brake problems.
The Australian, who ran straight on at Turn 4, was in and out of the Repsol Honda pits for much of the session, where mechanics were seen working on the front of his bike.
The reigning world champion finally moved into third place with ten minutes to go, but was 0.5s from team-mate Pedrosa and didn't beat the Spaniard's Friday best.
While Stoner worked on solving his issues, Yamaha Tech 3 team-mates Andrea Dovizioso and Cal Crutchlow had held third and fourth, before being pushed down a place by Stoner.
Lorenzo's team-mate Ben Spies ran off track at the final turn on his way to sixth place, but over one-second from Pedrosa.
Last weekend's podium finisher Alvaro Bautista took seventh for Gresini Honda, with Nicky Hayden the lead Ducati rider in eighth (+1.493s).
Hayden and team-mate Valentino Rossi both suffered lowside falls at turn one this morning - Rossi at the start of the session and Hayden at the end.
Rossi's tumble was followed by comical scenes as the Italian tried to prevent marshals pushing his undamaged bike away from the track.
The Doctor pulled the bib of a marshal to try and hold him back. Then, when that had no effect, put his hand on the marshal's shoulder to restrain him - much to the amusement of Rossi's mechanics watching in the pits.
Having successfully regained ownership of his Desmosedici, Rossi used the downhill run from the first chicane to restart his bike.
The seven time MotoGP champion, who hasn't won since Sepang 2010, finished the session in tenth place (+1.897s).
Rossi looked to try the hard tyre at the end of the session, while Hayden was halted by pit lane marshals after running out of time to rejoin the session.
Aleix Espargaro set the CRT pace in twelfth (+2.923s) for Aspar Aprilia, placing the Spaniard ahead of Karel Abraham's Cardion AB Ducati.
Avintia's Yonny Hernandez, who dislocated his collarbone last Sunday in Japan, did not ride this morning due to the pain and will miss the remainder of the Malaysian weekend.
