“I want to congratulate Valentino because to win nine world championships is an incredible achievement,” said Stoner. “I'm sure that if we continue to work like this ourselves we can put up a much stronger challenge next time.”
Stoner will start the Valencia season finale third in the championship and 11 points ahead of Dani Pedrosa (Honda), who was second in Sunday's race.
Despite his mid-season break, Stoner still has a slim chance of snatching second from Jorge Lorenzo, although Stoner would need to win at Valencia with Lorenzo failing to score.
Rossi has won six races this season, with Lorenzo and Stoner tied on four victories from the 16 rounds so far held.
Stoner's team-mate Nicky Hayden also produced a competitive display on Sunday, claiming his fourth top six finish of the year with fifth position.
“We'll take a top five, that'll work for us,” said Hayden. “I was quite excited when it started to rain because I've been on the pace with this bike in the wet this year and I felt I could do something special. Unfortunately I struggled a lot on the brakes in the beginning and a lot of guys came past.”
Seventh at the end of lap one, the American was involved in a series of exciting battles, passing Loris Capirossi and Toni Elias and doing his best to hold off title contenders Rossi and Lorenzo.
“I had a lot of fun passing and fighting with people, trying to close down the gap to the lead group, but I was just missing a little bit to really go with Rossi and Lorenzo and try to fight for the podium,” he said.
“When Vermeulen [sixth] came I knew he was a rain specialist so I pushed hard to make sure he didn't see a crack in the door and think he could push it open. I've been fourth here five times so I'm only one spot off my mark!
“After Phillip Island it seems every time we try to get something going we have huge bad luck but I'm thankful I have a team who keep working and never give up – we're trying to build something here together and we're making progress. Even this weekend we were consistently up near the top.
“I have to say congratulations to Casey and Valentino. It wasn't a terrible day for us either but now we go to Valencia and try to build on it again,” he concluded.