The German claimed his fifth win in a row to take a 90-point lead in the drivers' standings, with just 100 left to race for, starting in India next week.
"I'm blown away with today's race, I had a very, very poor start. I clipped a little bit the front wing, I couldn't go anywhere," he told BBC Sport.
"We looked after the tyres and had incredible pace towards the end and we managed to beat Lomain and Mark towards the end."
Lotus's Romain Grosjean led through the first pit stops before being overtaken by the Red Bull pair of Vettel and Mark Webber, but he did hold off Alonso's charge to claim his fourth podium finish of the season.
The Italian's 12-point haul in his Ferrari prevented Vettel from securing his fourth consecutive title in Japan, where Britain's Lewis Hamilton withdrew after nine laps and Jenson Button finished ninth.
Sauber duo Nico Hulkenberg and Esteban Gutierrez finished sixth and seventh respectively and just behind Kimi Raikkonen, who ensured that it would be a good day for Lotus by passing the chequered flag in fifth.
1. Sebastian Vettel (Red Bull)
2. Mark Webber (Red Bull)
3. Romain Grosjean (Lotus)
4. Fernando Alonso (Ferrari)
5. Kimi Raikkonen (Lotus)
6. Nico Hulkenberg (Sauber)
7. Esteban Gutierrez (Sauber)
8. Nico Rosberg (Mercedes)
9. Jenson Button (McLaren)
10. Felipe Massa (Ferrari)
11. Paul di Resta (Force India)
12. Jean-Eric Vergne (Toro Rosso)
13. Daniel Ricciardo (Torro Rosso)
14. Adrian Sutil (Force India)
15. Sergio Perez (McLaren
16. Pastor Maldonado (Williams)
17. Valtteri Bottas (Williams)
18. Charles Pic (Caterham)
19. Max Chilton (Marussia)
20. Lewis Hamilton (Mercedes) (Retired)
21. Giedo van der Garde (Caterham) (Retired)
22. Jules Bianchi (Marussia) (Retired)