The 2007 world champion was more than two tenths quicker than defending title holder Jorge Lorenzo's Yamaha at Motegi's Twin Ring circuit, with Italian Andrea Dovizioso third on the grid after clocking 1:45.791 for Sunday's race.
It was Stoner's 10th pole of the season and he holds a 44-point lead over Lorenzo in the standings with four races remaining this season.
"Everything has gone fantastically very well so far this weekend," said Stoner, winner of last year's race for Ducati.
"We've been fastest in all but one session. We tried a few different settings this afternoon and didn't really improve so we'll probably go back to this morning's setting for tomorrow.
"We'll have to watch the weather as this will affect the set-up, there's also a chance of rain so it could get complicated."
Sunday's race had been originally scheduled to take place in April but was rearranged after the deadly March 11 earthquake and tsunami, which triggered a nuclear meltdown at a power plant north of Tokyo.
Spaniard Marc Marquez took pole in the Moto2 category with a time of 1:52.067 in a Suter one-two-three while France's Johann Zarco was quickest for Derbi in the 125cc class in 1:57.888.
