Ferrari's Felipe Massa came second, 20.6 seconds behind Vettel, for the Brazilian's first podium finish since October 2010 with Japan's Kamui Kobayashi delighting his home crowd with third place for Sauber.
Only the third Japanese to stand on a Formula One podium, he was the first since Takuma Sato at Indianapolis in 2004. Only Aguri Suzuki, in 1990, had previously finished in the top three at Suzuka.
"Fantastic, unbelievable," he said, sharing a podium with Vettel for the first time since their Formula Three days and addressing the fans in Japanese.
Image: Race winner Red Bull driver Sebastian Vettel of Germany pours champagne over third place Sauber driver Kamui Kobayashi of Japan as they celebrate on the podium after the Japanese Formula One Grand Prix at the Suzuka Circuit in Suzuka, Japan, Sunday, Oct. 7, 2012.