Vettel reeled in his departing team-mate Mark Webber in the closing stages as well as Lotus driver Romain Grosjean, who wound up third for Lotus after a flying start at Suzuka. (Agencies)
But Fernando Alonso's fourth place means Vettel's celebrations stay on ice at least until India in two weeks, despite the German's career-best run of five straight race wins.
Webber began the race on pole for the first time this year but Grosjean's scorching start from fourth saw the Frenchman sneak into turn one ahead of the Australian.
Both men had their chances but ultimately Vettel proved too strong and, after roaring past Grosjean on the home straight on lap 41, went in front when Webber pitted for the third time and was never seriously threatened thereafter.
"Ichiban (first)!" whooped Vettel over the radio as he took the chequered flag for the ninth time this season. "You're the best team in the world. I love you guys. Yes! Ichiban!"
Webber's three-stop strategy cost him and, although he finally passed a determined Grosjean with two laps of the 53 left, it was too late to catch his team-mate and claim a first victory of the year in his last season in F1.
Grosjean finished on the podium for the fourth time this season by matching his third place at last week's South Korea race.
Vettel, on the brink of becoming only the third man to win four Formula One titles in a row after Michael Schumacher and Juan Manuel Fangio, now holds a 90-point lead over Ferrari's Alonso with 100 available from the last four races.
Vettel reeled in his departing team-mate Mark Webber in the closing stages as well as Lotus driver Romain Grosjean, who wound up third for Lotus after a flying start at Suzuka.