Hamilton started on pole and had to cut across the track to block off the move of Vettel.
However, the spark plug problem that had forced Ferrari to take the engine cover off minutes before the race had clearly not been fixed and he was forced to retire after just four laps.
Hamilton drove off into the Suzuka sunset but had two moments of really danger.
He was briefly threatened by the undercut of Max Verstappen, who drove brilliantly all day, and the Dutchman might have got the overtake done in the last two laps had Fernando Alonso and Felipe Massa not struggled to get out of the way quickly enough when being lapped.
Hamilton had never taken pole at the Japanese Grand Prix until this weekend but he was exemplary in Saturday’s qualifying session.
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His team-mate was second-fastest but a grid penalty allowed Vettel to start second on the clean side of the track in P2.
The Ferrari driver got the better start off the line but Hamilton was able to cover off the move up the inside and drive away from the field.
It quickly became clear that the problems Ferrari had sensed on the trip to the grid from the pits were not gone.
Vettel was down on power in the straights as first the Red Bulls and then the Force Indias drove straight past him and the German was told to retire the car after just four laps.