"Overall it's been a positive test and it's the end of a long season! I'm looking forward to going home now and having some rest, enjoying time with family and friends and preparing for the arrival of our child in February, then we'll be back in Sepang revitalised and ready for 2012".
Pedrosa and Stoner were the only riders under 1min 32sec, with lone factory Yamaha rider Ben Spies best of the rest on both days.
The Texan, beaten at the line by Stoner on Sunday, was 1.040sec from the top on day one, but closed to 0.531sec from Pedrosa on day two.
Spies rode 75 laps on Wednesday to add to the 73 he did on Tuesday, focusing on a new engine specification and electronics. Team-mate Jorge Lorenzo
is still recovering from his Phillip Island finger injury.
Fourth fastest on Wednesday was Monster Yamaha Tech 3 rider Cal Crutchlow (+0.743sec), with new team-mate Andrea Dovizioso
in fifth place, but nearly 1.5sec from Pedrosa.
The Italian concentrated on getting himself comfortable, while Crutchlow and his crew set about correcting a wheelie issue.
Then came the top Ducati of Valentino Rossi
in sixth (+1.525sec). The Italian continued work on the 'experimental' aluminium twin-spar frame (as used by the Japanese teams) which will be further adapted for the next test at Sepang.
Test rider Franco Battaini again rode Nicky Hayden's bike, after the American injured his wrist in Sunday's first turn pile-up.
Cardion AB Ducati rider Karel Abraham was just a fraction slower than Rossi at the end of his 1000cc debut, with Hector Barbera eighth on the timesheets during his first Pramac Ducati appearance.
Former Suzuki rider Alvaro Bautista made his Honda Gresini debut on Wednesday, riding Hiroshi Aoyama's 2011 800cc bike to ninth place (+2sec). New Moto2 world champion Stefan Bradl completed his second day on the LCR Honda 800 by lapping just 0.335sec slower.
LCR Honda is yet to announce its 2012 rider, but Bradl must surely be in contention.
The last four places on the 16 rider timesheet went to the new range of CRT motorcycles.
Carmelo Morales was best of privateer constructor entries, lapping 4.014sec from the top on a Team Laglisse's Suter-BMW.
Iván Silva and the Inmotec project were also on track, as was Moto2 rider Yonny Hernández with BQR's FTR/Kawasaki.
The session was briefly red flagged just before 2pm local time when Gapam's Federico Sandi crashed, but action resumed shortly after with the Italian escaping any harm.
All CRT machines, along with the 1000cc prototypes on track, tested Bridgestone's 2012 compounds too, with positive feedback.
The Sepang MotoGP test will start at the end of January.