Randy de Puniet improved to eighth on day two for Honda LCR, with Colin Edwards - who had complained about a lack of engine performance from his Monster Yamaha Tech 3 on Friday - only ninth.
The good news for Edwards was that factory Honda rider Andrea Dovizioso, whom Edwards is battling for fifth in the championship, was only eleventh, behind Gresini's Alex de Angelis.
Aleix Espargaro, riding in place of the injured Niccolo Canepa during his third Pramac Ducati appearance of the season, advanced from 17th and last on Friday to 14th on Saturday morning and then 13th in qualifying - just one place behind permanent Pramac rider Mika Kallio.
Chris Vermeulen will start his penultimate race for Suzuki from a lowly 14th, with Hayate's Marco Melandri (who, unlike most of the field, did not test at Sepang in the winter) 15th.
Tech 3's James Toseland - who had expected to rise up the order with a 'fresh' engine - a disastrous 16th, ahead of only Gabor Talmacsi (Scot Honda).
8. de Puniet
10. de Angelis