The Red Bull driver was far too good in Suzuka leading from start to finish, to add to his victory a fortnight ago in Singapore and close on Ferrari’s Alonso, who crashed out on the first lap.
Vettel won ahead of Ferrari’s Felipe Massa, who ended a long wait for a top three finish, while local hero Kamui Kobayashi claimed his first ever podium much to the delight of the home fans.
Alonso’s failure to claim any points, however, was the biggest story in the context of the championship race, as he was eliminated after hitting Kimi Raikkonen on the first corner before suffering a puncture.
“There is still a long way to go,” Vettel said with five races to go.
“Look at the last couple of races and since Spa (Belgium) - it’s been very much up and down.
“We don’t know what will happen in the next race, but let’s try and take the points. It’s been a long season with crazy racing.”
Drivers Championship Alonso, 194 - Vettel, 190 - Raikkonen, 157 - Hamilton, 152 - Webber, 134 - Button, 131 - Rosberg, 93 - Grosjean, 82