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Alonso's pre-race lead over reigning champion Vettel, chalking up his second win in a row and third of the season, was cut to four points from 29 with the Spaniard in danger of falling behind in South Korea next weekend.
"It was an important step today but there's still a long way," said Vettel after holding aloft the winner's trophy and making the familiar raised forefinger gesture as number one.
"These things happen and obviously you don't hope for those things to happen to yourself," he added of Alonso's exit into the gravel following contact with former Ferrari champion Kimi Raikkonen's Lotus.
"We have so many races, it could happen. We don't know what happens in the next race, it's good to take the points today."
Ferrari's Felipe Massa came second, 20.6 seconds behind Vettel, for the Brazilian's first podium finish since October 2010 with Japan's Kamui Kobayashi delighting his home crowd with third place for Sauber.
Only the third Japanese to stand on a Formula One podium, he was the first since Takuma Sato at Indianapolis in 2004. Only Aguri Suzuki, in 1990, had previously finished in the top three at Suzuka.
"Fantastic, unbelievable," he said, sharing a podium with Vettel for the first time since their Formula Three days and addressing the fans in Japanese.
Massa seemed so out of practice at being on the podium that he knocked over his bottle of champagne, spilling some of it on the stage before he had a chance to shake the bottle as he collected his trophy.
The victory was Vettel's third from pole in Suzuka in the past four years and he also set the fastest lap after leading from start to finish in the Suzuka sunshine with the team warning him to be careful.
In truth, he had nothing to worry about with Massa far behind and Kobayashi fighting to keep McLaren's Jenson Button behind him right to the finish. Button, last year's winner, crossed the line 0.5 adrift of the Sauber.
McLaren's 2008 champion Lewis Hamilton was fifth ahead of Kimi Raikkonen in the Lotus and Germany's Nico Hulkenberg for Force India.
Venezuelan Pastor Maldonado scored his first points since he won the Spanish Grand Prix, ending a run of nine races without scoring for Williams.
Australian Mark Webber was ninth for Red Bull after starting on the front row following Red Bull's first one-two of the season in qualifying, and then having to fight back from last place after a collision with Frenchman Romain Grosjean's Lotus at the start.
Grosjean, banned for the Italian Grand Prix in September, was handed a stop-go penalty for the incident. Webber branded him a "first lap nutcase" and suggested it might be time for him to take another "holiday".
Australian Daniel Ricciardo took the final point for Toro Rosso, denying Michael Schumacher a top 10 placing in what was the German's final Japanese appearance before retirement at the end of the season.
The safety car was deployed after the first lap with Alonso trudging back to the paddock after his Ferrari went spinning onto the gravel and then back on to the track facing the oncoming cars.
"Five great races coming! If the enemy thinks in the mountains, attack by sea, if they think in the sea, attack by the mountains," the Spaniard's official Twitter feed declared.
Schumacher's team mate Nico Rosberg also retired at the start after a collision with Williams' Brazilian Bruno Senna, who was given a drive-through penalty.