Stoner lost out during a tense three-way battle for pole with Honda star Pedrosa and Tech 3 Yamaha's
Colin Edwards, all three dipping under the 1min 33secs mark and being separated by just 0.347secs by the end of the qualifying hour.
"First of all I want to say congratulations to Pedrosa for a great lap. Myself and Dani go back a long way and he's been riding phenomenally well this season so he deserves to be on pole," said Stoner. "Having said that, I think I should have been there instead today! Basically I made a mistake towards the end of my best lap and I think it cost me pole position, so I have to accept responsibility for that."
Nevertheless, Stoner still secured a front row start and is confident that he can fight with Pedrosa, Edwards and fourth fastest
Valentino Rossi for victory in Sunday's race.
"From my point of view the qualifying position is not important so long as we're in touch and a front row start gives us a good chance," said Stoner, who has been losing time in the final sector of the lap. "The most important thing is that we're in good shape in race trim and if it stays dry tomorrow then we could be in for a good battle.
"Pedrosa and Edwards look like they will be on the pace and you always have to expect Valentino to join in too so hopefully the weather stays dry for the fans and we get a good race and a good result," added the Australian.
The atmosphere was very different on the other side of the Ducati Marlboro pit, with
Marco Melandri's post-Shanghai optimism crushed by another tough session at Le Mans and just 17th on the grid.
