The result ended Stoner's hopes of retaining his title, as Rossi reclaimed the championship for the first time since 2005.
Stoner has been racing with an injured wrist in recent rounds, having aggravated a long-standing fracture. He is waiting until the end of the season before undergoing the surgery he requires, but conceded that he lacked the fitness to keep up with Rossi at Motegi.
"At the beginning of the race, everything felt quite good," said Stoner.
"I was comfortable staying at that pace, but then I started to get a little bit tired changing direction, and I was having to close the gas coming out of corners to get into another one, just because I didn't have enough physical force to change direction on the bike.
"So my lap times started to slow and Valentino came past. I thought I could stay behind for a while because I knew we could go fast enough, I was just having to keep enough breathe in.
"We started to lose ground, I was trying to hold on, and about three-quarters of the way through I didn't give up, but backed off the pace a little bit because I just couldn't keep it up.
"With about five laps to go I started to feel a little bit better in my condition so I pushed a bit harder and I was doing some reasonable lap times, and then I just made a mistake and that was it, race over again.
"We gave it an effort today, but hopefully these next few races and next year we'll come back stronger."
Stoner said he was not downcast about handing the title to Rossi, as he had known for some time that he was likely to relinquish his crown.
"When you know the championship's going to go, I think some people over-react and then try and do everything to keep it," he told BBC television.
"But when it's gone, it's gone, and you just concentrate on every race. We've been giving 100 per cent these last races. I've crashed at a couple, which has been really disappointing, but I got myself together again at Indianapolis and then today I felt really good in the beginning."
Although the Australian won the Qatar season-opener, he then endured several difficult races before reviving his title hopes with three consecutive mid-season victories. However he lost that momentum after coming second to Rossi in a spectacular race at Laguna Seca, and subsequently crashing out when leading at the next two races.
That allowed Rossi to make a break, and the Italian has now won five consecutive GPs. But Stoner is optimistic that he can strike back at his home race next weekend.
"It's been a difficult season for us," he said. "We've found some big improvements, we've learnt how to go a lot faster. This track I don't feel suits our package entirely, but we did a much better job than we did last year, so we've got a good chance at Phillip Island."
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