Stoner, who fell heavily on Friday, almost fought his way onto the second row of the grid, but lost vital tenths after running wide on his best lap.
His frustration at a difficult day was made clear when he lashed out at former team-mate
Loris Capirossi as the pair excited the final turn.
Nevertheless, Stoner believes he's in 'a bit better shape' for the race, although he isn't quite sure what to expect from the 27 lap encounter.
"Things haven't really been going too well for us here," began Casey. "We managed to go pretty much as quick as we'd gone all weekend early in the first session today but didn't really improve from there so that's disappointing.
"Qualifying could have been a lot better - I had a good lap going but unfortunately with the settings not being perfect the front just pushed me wide in one turn and I lost a good few tenths of a second, otherwise we would have been on the second row.
"We should be in a little bit better shape for the race - we got a decent pace and rhythm but we're not quite at the point where we need to be.
"I think there are a lot of guys in a similar situation to me, we're all struggling with the same thing so we'll have to wait and see what we can all do in the race tomorrow but we'll give it some!" he concluded.
Team-mate
Marco Melandri's afternoon was about as bad as it gets, as the Italian tried in vain to turn around a disappointing start to the season at the most hostile circuit on the calendar for his bike.
The former 250cc world champion fell midway through the afternoon hour and his miserable day was made complete when he qualified 18th and last on the grid.
"I had a crash in this afternoon's qualifying session and it was strange because I wasn't pushing very hard. The front felt a bit nervous and suddenly folded," explained Marco.
"We went straight back out with the other bike on qualifying tyres but the setting was a little different and I really struggled with it. It's a shame because my last run this morning went quite well but when we dialled the same settings in this afternoon the feeling wasn't the same.
