Alonso was forced to retire on the first corner after being hit by Romain Grosjean, who was made to serve a 10-second penalty for the incident.
There was no battle for the win as the German led from pole to finish, setting countless fastest laps along the way, to complete a perfect race for 25 points.
The McLarens of Jenson Button and Lewis Hamilton were never in contention for the win in fourth and fifth, although Button was in a battle with home favourite Kamui Kobayashi for third, but the Japanese just about held on for an incredible podium finish.
Alonso's teammate Felipe Massa was comfortable in second after working through the field from 10th on the grid, a result that should boost his poor season so far.
Vettel, however, was untouchable and the German was sublime to move just four points behind Alonso to set up a thrilling end to the Formula 1 season.