Vettel, racing on the Fuji Speedway where he wrapped up the 2011 driving title, jumped into the lead early and never relinquished it. It was the Red Bull's driver third race win in 2012, second in a row, and 24th Grand Prix victory overall.
Vettel finished the 53 laps around the 3.6-mile Fuji Speedway in 1 hour, 28 minutes, 56.242 seconds. Ferrari's Felipe Massa was second, 20.6 seconds back of Vettel while Kamui Kobayashi, from Sauber, took third about 4 seconds behind. Fourth went to McLaren's Jenson Button, who finished 25 seconds behind Vettel.
Alonso, leading the Ferrari team, tangled with Lotus's Kimi Raikkonen on the first corner and suffered a punctured left rear tire and didn't pick up any points in this race.
That left him with 194 points while Vettel's 25 won Sunday gives him 190 in the drivers' standings. Raikkonen, who ended up with at the Japanese Grand Prix, is third with 157 and McLaren's Lewis Hamilton, who was fifth, comes in with 152.
There are five races remaining on the 2012 Formula 1 schedule, including Korean Grand Prix on Oct. 14.