Jorge Lorenzo overcame Dani Pedrosa for pole position
The Factory Yamaha star, who will start Sunday's race with a 28-point advantage over Pedrosa, set the pace at the start and end of the hour - setting a new lap record on his 23rd and final lap to finish 0.194s clear of Pedrosa.
Unlike most of his pole rivals, Lorenzo opted to use the soft front tyre - as well as the soft rear used for much of the weekend - to set his fast laps.
Repsol Honda's Pedrosa held pole during the middle stages, with Yamaha Tech 3's Dovizioso then emerging as a surprise challenger.
The hard-braking Italian snatched pole with 15 minutes remaining, then again with just two minutes to go, before Pedrosa and then Lorenzo moved ahead.
Nevertheless, third place marks Dovizioso's first front row start since Indianapolis and he was only 0.233s slower than Lorenzo.
Casey Stoner again spent large parts of the session trying to solve set-up issues with his Repsol Honda, and didn't post a flying lap until 13 minutes into the hour.
Fifth during the middle part of the session, the reigning double world champion - who made his comeback from ankle surgery last weekend in Motegi - didn't improve after his 16th of 21 laps and finished the session in fourth place, +0.477s.
Dovizioso's team-mate Cal Crutchlow moved into fifth place, 0.8s from pole, on his final lap. A fraction behind the Englishman was Lorenzo's team-mate Ben Spies, who will complete the second row.
Pramac Ducati's Hector Barbera again made good use of a tow to be the top Ducati rider in seventh place (+0.960s), with Honda LCR rookie Stefan Bradl the first rider outside one-second of pole.
Nicky Hayden led the factory Ducati challenge in ninth (+1.192s) on another tough weekend for the team, with team-mate Valentino Rossi only eleventh (+1.449s), the positions and time difference signally no relative improvement since winter testing at the track.
Starting between the factory Desmosedicis will be Alvaro Bautista, who missed the end of the session after falling from his Gresini Honda.
Aleix Espargaro held off Aspar team-mate Randy de Puniet by over half a second to be the leading CRT rider, with both lapping quicker than Karel Abraham's Cardion AB Ducati.
Avintia's Yonny Hernandez, who dislocated his collarbone last Sunday in Japan, has withdrawn from the remainder of the Malaysian weekend due to pain from his injury.
