Stoner, the 2007 world champion who will be starting his 150th grand prix in all categories on Sunday, made sure of his fourth pole in six races with a quickest lap of two minutes 02.020 seconds.
Italy's Marco Simoncelli, also on a Honda, was second fastest in a dry session ahead of Yamaha's reigning world champion Jorge Lorenzo of Spain.
Stoner can become the first Honda rider to win three successive MotoGP races since Valentino Rossi in 2003 and few would bet against the 25-year-old after he dominated Friday practice in mixed conditions.
"Looking at the way we went this weekend, it doesn't really matter what conditions tomorrow brings," said the Australian, knowing it could be wet on Sunday. "I am definitely going to prefer dry...but we feel ready for any conditions." "I felt we got quite lucky with pole position today, we tried a couple of things with the bike...we changed the front a little bit and on my best lap I lost the front two or three times," he added.
"One of them was very small but two were more than I'd like to push." Simoncelli, who started the last race in Spain on pole but faded to finish sixth, hoped to be Stoner's main adversary in the absence of Honda's injured Spanish rider Dani Pedrosa.
"Here I have a better feeling with the bike than in Barcelona," said the Italian.
"I am feeling ready to fight for the podium and victory tomorrow." There was bad news for Crutchlow, the sole British rider in the championship, who looked sure to miss his home race after falling on only his second lap and fracturing his left collarbone.
Officials said the Yamaha Tech3 rider, who clutched his shoulder in pain as he lay on the grass before being taken away on a stretcher, was also suffering from concussion.
After finishing seventh in Barcelona last weekend and setting the sixth fastest lap in Friday's practice, the British rookie had hoped to shine in front of his home fans at the circuit where last year he won two superbike races, Crutchlow's American team mate Colin Edwards, who broke his right collarbone in practice last week for the Spanish Grand Prix, qualified an impressive eighth.
Italian great Valentino Rossi was a disappointing 13th on his Ducati, 3.7 seconds off the pace. Spaniard Maverick Vinales took his first pole in the 125cc category, the 16-year-old beating championship leader and compatriot Nicolas Terol into second place.
France's Johann Zarco, who was denied a first victory in Spain last weekend after being disqualified for an illegal overtaking maneuver on Terol on the final bend, starts third.
