The Australian has been the king of one-lap pace this year and again underlined his prowess on Saturday, his best lap of one minute 31.861 seconds enough to secure his 12th pole of the campaign.
Stoner's lap, posted on a drying track after a rain-affected weekend to this point, means he equals five-time 500cc world champion Mick Doohan's record for most poles in a season.
The Repsol Honda rider, who wrapped up his second MotoGP crown on home soil in Australia last month, lapped over a second quicker than team-mate Dani Pedrosa in second, while the factory Yamaha of Ben Spies will line up third for the final race of the season.
"Of course I'm really happy with pole position today, I'm still hungry to win and get pole positions, after all this is why I line up to go racing," said Stoner.
"Winning the championship is the bonus at the end of the season, but I still try my best in every session and every race.
"The feeling in the bike was pretty good. Now we'll have to see what the weather does tomorrow and take it from there, but we remain confident."
Pramac Racing's Randy de Puniet will start from the front of row two, posting a time just 0.061secs slower than Spies, while Alvaro Bautista (Rizla Suzuki) will line up fifth and Valentino Rossi (Ducati) sixth.
Ducati's Nicky Hayden heads the third row from Andrea Dovizioso (Repsol Honda) and Hector Barbera (Mapfre Aspar), while Karel Abraham (Cardion AB Motoracing), Britain's Cal Crutchlow (Yamaha Tech 3) and Pramac's Loris Capirossi make up row four.
Sunday's race is the first since the death of Italian rider Marco Simoncelli in an accident at the Malaysian Grand Prix a fortnight ago.
MotoGP organisers confirmed there would be a ceremony at 10.10am local time on Sunday to honour the 24-year-old Italian, who rode for the Gresini Honda team.
All the riders from the MotoGP, Moto2 and 125cc classes will depart the pit lane en masse and complete a lap of the track in honour of Simoncelli.
The procession will be led by Simoncelli's Honda Gresini RC212V bike, which will be ridden by 1993 world champion Kevin Schwantz.
A statement by MotoGP organisers added: "As the riders round the final corner of the circuit and approach the finish line they will stop just short, with local authorities and representatives of MotoGP's governing bodies congregating on the other side of the finish line alongside Simoncelli's family and members of the Gresini team.
"Once the bikes have taken up their positions on the start/finish straight a two-minute Valencian Mascleta (a traditional firecracker display) will take place."