Alonso suffered a puncture when he was hit from behind by Lotus's Kimi Raikkonen.
Japanese Grand Prix Top 10
1. Sebastian Vettel - Red Bull 1:28.56
2. Felipe Massa - Ferrari +00:20.64
3. Kamui Kobayashi - Sauber +00:24.54
4. Jenson Button - McLaren +00:25.54
5. Lewis Hamilton - McLaren +00:46.49
6. Kimi Raikkonen - Lotus +00:50.42
7. Nico Hulkenberg - Force India +00:51.16
8. Pastor Maldonado - Williams +00:52.36
9. Mark Webber - Red Bull +00:55.68
10. Daniel Ricciardo - Toro Rosso +01:07.92
Ferrari's Felipe Massa took second ahead of Sauber's Kamui Kobayashi.
"I knew behind me there was a crash and I saw a Ferrari was out but wasn't sure which," said Vettel. "Halfway through I was looking to see the others and I saw there [Ferrari] car still racing Felipe, I didn't know what happened to Fernando.
"The atmosphere has been unbelievable all weekend. There has been so much support, the stands have been full and that really makes our job feel very special.
"When you're dreaming at night, you dream one day about racing a car like that. The balance was so good and that's why there was a gap to behind."
"I was clever on the first corner to manage to avoid the accident and the pace was really good," said Massa.
"I was quicker than Jenson [Button], then I was able to pass him and then Kamui [Kobayashi] so for sure it was a better race than what I expected.
"Unfortunately Fernando isn't here on the podium fighting for the championship but hopefully we can keep on pushing."
'Strange' car problems for McLaren duo at Japanese Grand Prix
The second McLaren of Lewis Hamilton was fifth, ahead of Raikkonen, who was forced to fend off Force India's Nico Hulkenberg and Williams's Pastor Maldonado in the closing laps.
Red Bull's Mark Webber fought up from the back of the field after being hit from behind at the first corner to take ninth ahead of Daniel Ricciardo, who held off
Michael Schumacher's Mercedes
in the last few laps.
For Vettel, it was one the most comfortable victories of the year.
He converted pole position
into a lead at the first corner and streaked away into a race of his own.
It was the first time a driver has taken back-to-back victories this season, and Vettel's third win in four years in Japan. The 25-year-old now looks a strong bet to win his third consecutive world title.
The Red Bull is a faster car than the Ferrari, in which Alonso has been fighting a rear-guard battle for some time.
“Thank you very much everyone. This is my first podium, and in Japan. Fantastic, unbelievable”
Alonso said of his retirement: "Kimi touched me a little bit in the rear and I had a puncture. It is a little sad but we need to concentrate and think about [the next race in Korea] next week.
"We need to keep working well and not making mistakes. Nothing we can do. Thanks to this consistency we are leading the championship. The others make mistakes, we need to avoid this."
Raikkonen is in third place in the championship, 33 points behind Vettel and five points ahead of Hamilton.
Red Bull's Mark Webber, who finished ninth, is effectively out of contention, 60 points behind Alonso with a maximum of only 125 still available.
Last 10 winners of Japanese GP
2011 - Jenson Button, McLaren
2010 - Sebastian Vettel, Red Bull
2009 - Sebastian Vettel, Red Bull
2008 - Fernando Alonso, Renault
2007 - Lewis Hamilton, McLaren
2006 - Fernando Alonso, Renault
2005 - Kimi Raikkonen, McLaren
2004 - Michael Schumacher, Ferrari
2003 - Rubens Barrichello, Ferrari
2002 - Michael Schumacher, Ferrari
2001 - Michael Schumacher, Ferrari
The turning point of the race and perhaps the entire championship came on the run to the first corner.
Raikkonen ran slightly off the road and as he rejoined his front wing touched Alonso's left rear tyre, which punctured and tipped the Spaniard into a spin as he turned into the first corner.
Meanwhile, Lotus's Romain Grosjean put Webber into a spin, and in a separate incident Williams's Bruno Senna hit Nico Rosberg's Mercedes.
Rosberg was forced to retire, but Webber, Grosjean and Senna were all able to rejoin at the back of the field after pit stops, with Webber driving a quietly determined race to get back up into the points in ninth place.
The safety car was sent out while the debris was cleared away, with Massa up into fourth place behind Vettel, Kobayashi and Button.
Kobayashi on "amazing" result
Massa passed both his rivals by making his first pit stop later than they did, partly thanks to being able to start the race on new tyres while those who made it into the top 10 in qualifying had to start on the tyres that had used to set their grid time.
The Ferrari initially made inroads into Vettel's lead, but a couple of fastest laps from the Red Bull driver made it clear there was plenty of pace in reserve.
Behind Massa, Kobayashi held off a determined challenge from Button, who was battling with a gearbox that was intermittently slipping into neutral in the first three laps after each of his two pit stops before righting itself.
Button closed on Kobayashi before their final pit stops, but lost out by making his earlier than the Japanese.
The McLaren closed in again in the final 10 laps but Kobayashi was able to hold him off.
"Thank you very much everyone. This is my first podium, and in Japan. Fantastic, unbelievable," said Kobayashi after the race.
Japanese Grand Prix 2012, day three
Sunday, 7 October: Race highlights on BBC One 14:05 BST and online. Repeated Mon 8 Oct at 00:35 BST on BBC Two.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.