Chasing his fourth win in Qatar in five years, Stoner chalked up his 27th career pole with a lap of one minute 54.137 seconds, 0.205 quicker than Spanish team mate Dani Pedrosa in second place.
"The consistency we've shown in pre-season testing is something that's really given us a lot of confidence," said the 2007 champion, who won in Doha in 2007, 2008 and 2009.
"The team's done a fantastic job, they've done everything right and we've made small steps in every session and slowly got the bike to a place where we really enjoy it," added the 25-year-old who raced for Ducati last year.
Yamaha's Spanish world champion Jorge Lorenzo took the third and final front row slot, 0.810 slower than the pole time.
Italian Marco Simoncelli was fourth on a Honda, ahead of Yamaha's American Ben Spies and Spain's Hector Barbera on a Ducati.
"There were some really impressive lap times out there tonight in the session," said Lorenzo. "We are still quite far behind the front but our goal is to finish on the podium and that is in my mind for tomorrow."
"My race pace is pretty good; I think I can keep running 1:55.7s or maybe 1:55.8s. We will finalise our set up in warm-up and try to achieve that tomorrow."
Cal Crutchlow, the former world superbike rider who is the sole Briton in the top category, will line up an impressive eighth for his MotoGP debut despite a finger injury.
Italy's seven-time champion Valentino Rossi qualified a distant ninth for what will be his first race with Ducati.
Rossi, Lorenzo's Yamaha team mate last year, is still struggling from a shoulder injury that has hampered his pre-season testing.
Sunday's race will have just 16 riders after Suzuki's Spanish entry Alvaro Bautista broke his left thigh bone in Saturday practice.
Germany's Stefan Bradl took pole in the Moto2 category with Spain's Nicolas Terol fastest in 125cc qualifying.
Nini/timesofindia
