Stoner led all three free practice sessions, despite a spectacular tumble on Saturday morning, and then - fearing rain - used one of his qualifying tyres after just 17 minutes of the afternoon hour, putting him on provisional pole.
But rain never arrived and, with only one run left, Stoner lost out to both Valentino Rossi and Dani Pedrosa by the chequered flag.
"Qualifying was probably our worse session so far this weekend [but] the front row or the second row is okay here," said home hero Stoner. "We went out quite early with a qualifying tyre because every other session had been interrupted by rain so we thought we'd get in a decent qualifying lap in case the rain started, but the rain never came, so it probably wasn't the best idea as we only had one qualifying tyre left for the end of the session.
"We felt like we could've gone at least a second quicker than that, unfortunately I got held up by other riders on both of my laps. That last lap Tamada got in my road big time and pretty much blew the lap to pieces, then I made a small mistake that added a few more tenths," revealed the 21-year-old, who was left 0.615secs from pole. "Looking at the race tomorrow we're pretty happy, we think we've got a very good setting at the moment and we're happy with our race tyres. We're running pretty hard tyres, like everybody else, and everything's looking really good for us."
Team-mate and Japanese GP winner Loris Capirossi also used an early qualifying tyre on his way to setting the fifth fastest time.
"I'm happy with fifth fastest because we have worked very well as a team. We used the settings we used during our winter tests here and they are working well," said the Italian. "We made good use of the qualifying session to do all the tests that we hadn't been able to do yesterday or this morning due to the rain. I rode a lot of laps this afternoon, 14 or 15 in a row, which helped me to understand what we need to do tomorrow. I have quite a good feeling with the bike, even if conditions aren't the best because it's very cold. I think we can do well tomorrow. Starting from the second row is good enough and if we get a good start we will see what happens."