Australian Casey Stoner won the race but the 30-year-old Italian secured the title by coming in third on his Yamaha. Spain´s Dani Pedrosa was second.
Rossi said he was delighted to seal the championship title with one race to go, in Valencia on November 8.
"With one round to go, I have clinched the world title. I thank all the people who helped me achieve this achievement. We did some great fight," he said.
"Today´s race went a bit like how the season has gone because we were so fast on the dry tyres, but right before the start of the race it started to rain so we had to go out on the track without any wet setting," said Rossi.
"It´s a great achievement, and for me it´s the ninth championship, the seventh in MotoGP," he said.
Rossi paid special tribute to his Yamaha team-mate Jorge Lorenzo. The 22-year-old Spaniard finished the race fourth but had been the only rider still in contention for the world title.
But Lorenzo, who was second on the grid, ended up starting from the back of the field after his number one bike could not start in the pits. He had to ride his spare machine.
"Throughout the season I had great rivals, at the end especially Jorge my team-mate, who stayed very close to me, and we had some great fights. He´s a great rival so congratulations to him," said Rossi.
"But we are on the top and now we´ll relax and try to take in this achievement. The ninth championship is great. I´m so happy," he added.
Rossi pulled a wheelie over the finish line to celebrate his latest success.
Heavy rain delayed the start of the race by 35 minutes and played a major part when the action finally got underway.
Rossi started on pole but failed to hold his lead and went wide into the first corner with a pack of riders, led by Pedrosa and Stoner, who had overtaken him with ease.
Stoner, fresh from victory at Phillip Island, passed Pedrosa and never looked back, romping home with something to spare.
The 2007 champion here in Sepang, Stoner came home in 47min 24.834sec, while Pedrosa was adrift at 14.666sec and Rossi narrowly behind him.
"I got a good start," said Stoner, who began in the second row on the grid.
"I did not expect to pull such a gap. I am happy with the pace. I am looking forward to the race in Valencia."
Pedrosa admitted that it was tricky to keep second position with Rossi snapping at his heels.
"It was a tough race until the end because Rossi was pushing me hard," he said.
Earlier, Japan´s Hiroshi Aoyama, riding a Honda, led from the start to win the 250cc race.
Birthday boy Aoyama, who now leads the 250cc championship standings with 252 points, clocked 42 minutes, 55.689 seconds in the 20-lap race after starting from pole position.
Spain´s Julian Simon won the 125cc on an Aprilia.
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