Australia's Casey Stoner made it back-to-back race wins by taking the checkered flag on his Ducati, with Honda's Dani Pedrosa second.
Yamaha's Rossi finished third after his Italian compatriot Andrea Dovizioso lost control of his Honda with seven laps to go in the 21-lap race at the Sepang circuit. The race was delayed by 35 minutes to allow the track to dry after a thunderstorm.
Rossi retained his world title with one race to spare and heads the championship standings with 286 points. Teammate Jorge Lorenzo, who finished fourth at Sepang, trails in second place with 245 points.
Rossi was relieved to have sealed the world title chase before heading to Valencia.
"We have been so fast on a dry track, but it started raining here from the start and we had to go in without a dry setting. But we did some great fight to win the world title with a race to spare," Rossi said.
Stoner was glad to pull off another win for Ducati after missing three earlier races because of illness.
"I had a good start at the first turn and I do not expect to pull a gap after that. I can't ask for more after how the season went. It's nice to come back and get a result like this," said Stoner, the only rider to win in all classes at Sepang.
Rossi, 30, also has 250cc and 125cc titles to his name, making him a nine-time world champion. His seven titles in the premier class puts him only behind Italy's Giacomo Agostini, who won eight between 1966 and 1975.
Meanwhile, Japan's Hiroshi Aoyama celebrated his 28th birthday in style by winning the 250cc race, moving to the brink of clinching the championship.
Aoyama, on a Honda, prevailed after a head-to-head duel at the Sepang circuit with Italian Marco Simoncelli, who eventually placed third after a photo finish was required following Spaniard Hector Barbera's late surge.
The Japanese rider, who won by 6.397 seconds, extended his lead at the top of the championship standings to 21 points over Simoncelli and only needs a tenth-placed finish or better in the final race in Valencia in two weeks to secure the 2009 world title ahead of the Italian.
In the 125cc class, Spaniard Julian Simon, who was crowned world champion in Australia last Sunday, earned his sixth win of the season after beating his Bancaja Aspar teammate Bradley Smith.
Simon held off Smith's challenge at the last corner but Smith still secured second position in the world championship despite riding with a broken bone in his right foot from a qualifying crash Saturday.
