The Repsol Honda rider, the winner of the past three races and seven in total this season, took top spot with a time of one minute 33.138 seconds, a mark which bettered his own lap record around the circuit set in 2008.
The pole was the 30th of Stoner's MotoGP career and the Australian said: "It's been a pretty good weekend for us here, steadily improving the bike each session.
"It will be a tough race. I'll try to get a good start but there are a few more overtaking opportunities here at Misano, it's not a track with only one line."
Stoner's eighth pole of the year came at the expense of title rival Jorge Lorenzo (Yamaha), whose late bid for top spot fell short by just 0.120secs.
"Today has been a good day for us," said reigning world champion Lorenzo, who trails Stoner by 44 points with six races remaining.
"We wanted pole position but the first row is a good start for tomorrow.
"I think we can be competitive tomorrow and try to finish in front of Casey so that's our aim. The weather conditions are being very tough this weekend, it might even rain tomorrow. The race will be very difficult in all aspects."
In a session run in sweltering heat, Stoner's team-mate Dani Pedrosa, who won this race from pole position last season, took third place in a time of 1:33.318.
The second factory Yamaha of Ben Spies will start from the front of the second row, where he will be joined by Marco Simoncelli (Honda Gresini) and Andrea Dovizioso (Repsol Honda).
Colin Edwards (Yamaha Tech 3) will line up seventh ahead of Alvaro Bautista (Rizla Suzuki) and Hector Barbera (Mapfre Aspar), with Hiroshi Aoyama (Honda Gresini) completing the top 10.
Britain's Cal Crutchlow (Yamaha Tech 3) suffered a late crash as he managed only 13th, one place ahead of Randy de Puniet (Pramac Racing) who also recovered from an accident earlier in the session.
It was a miserable day for the factory Ducati riders, Valentino Rossi, normally so strong at Misano, managing just 11th, while team-mate Nicky Hayden took 15th.