The Ducati rider, fifth in the title race but 141 points behind Lorenzo, posted a time of one minute 48.942 seconds with Lorenzo 0.309 secs adrift.
Andrea Dovizioso, third in the standings, trailed in eighth, one place behind Valentino Rossi.
Stoner's pole is his first since the season-opening race in Qatar.
And the Australian admitted he has had to endure a difficult campaign, with other riders making the running in the title race.
"I've had plenty of weekends where things have gone well up to the race," the 24-year-old said.
"We changed my riding position on the bike, tried some other things and got some more grip. The rear's a bit more stable and seems to be working well.
"I feel pretty confident on the bike." However, the real attention on Sunday will be on Stoner's front-row companions, with Yamaha's Lorenzo and Repsol Honda rider Pedrosa continuing their battle for the 2010 title.
Lorenzo, who holds a 53-point advantage with six races remaining, admitted that he struggled for power on the Spanish track.
"We really lost so much power on the main straight and also in every acceleration, especially compared to the Hondas," he said.
"But this is the bike we have now and the bike we have tomorrow so we have to do the best we can."
Pedrosa had looked set to steal pole on his final lap until running wide. Behind him, Ducati's Nicky Hayden, Yamaha Tech 3 rider and Honda's Randy de Puniet make up the second row.
However, Yamaha's seven-time world champion Rossi and Honda's Dovizioso endured a frustrating session, both more than a second behind Stoner.
In Moto2 qualifying, Scott Redding was pipped by Andrea Iannone, who took pole with his final lap.
Redding was racing despite being injured a fortnight ago in the crash that killed Japanese rider Shoya Tomizawa.
As a mark of respect for Tomizawa, all riders will wear his number 48, with the number then being retired.
Aragon MotoGP qualifying result:
1 Casey Stoner (Aus) Ducati 1min 48.942secs
2 Jorge Lorenzo (Sp) Yamaha 1:49.251
3 Dani Pedrosa (Sp) Honda 1:49.343
4 Nicky Hayden (US) Ducati 1:49.506
5 Ben Spies (US) Yamaha 1:49.565
6 Randy De Puniet (Fra) Honda 1:49.952
7 Valentino Rossi (Ita) Yamaha 1:50.017
8 Andrea Dovizioso (Ita) Honda 1:50.046
9 Marco Simoncelli (Ita) Honda 1:50.088
10 Hector Barbera (Sp) Ducati 1:50.323
11 Colin Edwards (US) Yamaha 1:50.440
12 Alvaro Bautista (Sp) Suzuki 1:50.523
13 Aleix Espargaro (Sp) Ducati 1:50.537
14 Marco Melandri (Ita) Honda 1:50.580
15 Hiroshi Aoyama (Jpn) Honda 1:50.836
Moto2
1 Andrea Iannone (Ita) Speed Up 1min 55.148 secs
2 Scott Redding (GB) Suter, 1:55.189.
3 Alex De Angelis (San) Motobi, 1:55.194.
125cc
1 Marc Marquez (Spa) Derbi 1min 59.335secs
2 Sandro Cortese (Ger) Derbi 1:59.898
3 Nicolas Terol (Spa) Aprilia 1:59.970
Source: http://news.bbc.co.uk/sport2/hi/motorsport/motorbikes/9012050.stm
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