In a race in which most of the action was over within the first half-lap, Sebastian Vettel moved within four points of Fernando Alonso in the fight for the world championship.
While the Red Bull driver dominated, Ferrari's leader found himself a first-corner victim for the second time in three races.
As Vettel sped into a lead he never relinquished, Alonso had a brush with Kimi Raikkonen and spun out of the race with a punctured rear tyre. At the same time, bad boy Romain Grosjean hit Vettel's team-mate Mark Webber.
"I had no space on the right – I had [Jenson] Button there I think – on the left I had Kimi and I don't understand why Kimi didn't lift off as there was no room and it was only the first corner," Alonso said.
Webber was incandescent about Grosjean, who was recently banned after causing the accident at the first corner in Belgium in which Alonso was also taken out. Sources say the Australian even made an angry visit to the Lotus hospitality cabin.
"It was the first-lap nutcase again, Grosjean," Webber said. "The rest of us are trying to fight for decent results each weekend but he's trying to get to the third corner as fast as he can at every race. It makes it frustrating because a few big guys obviously suffered from that today. Maybe he needs another holiday.
"He needs to have a look at himself. It was completely his fault. How many mistakes can you make, how many times can you make the same error with first-lap incidents?"
The safety car was deployed for just two laps, and thereafter Vettel was untouchable as he scored a victory that brought him level with the Argentina legend Juan Manuel Fangio's 24, and his points tally this season to 190 compared to Alonso's 194. "Nothing could be better than this," the world champion said. "You come across these races and weekends very rarely.
"The start was the key as Kamui [Kobayashi] came past Mark [Webber] already and then Mark got into trouble. I just focused on what I was doing and it was crucial not to be in the pack. After that I had a very good race car.
"You dream at night that one day you'll be able to race a car like that. The balance was fantastic every lap, that's why I was still pushing hard at the end."
Behind him, local hero Kobayashi valiantly held second place ahead of Button and Felipe Massa, but the Brazilian leapfrogged both rivals during the first pit stops to snatch a second place that he kept to the finish as he salvaged something for Ferrari. It was his first podium since South Korea in 2010 and the performance will almost certainly confirm his place with the team for 2013.
"The pace of the car was very good and I was quicker than Jenson and Kamui," Massa said. "My race was so much better than I expected and I'm very happy with it.
"It's fantastic to be on the podium and I'll keep pushing hard to be on it at every race, not every two years! It's nice, a relief to be able to show that we are still here, able to fight for victory or a podium position."
Kobayashi said: "My team-mate [incoming McLaren driver Sergio Perez] had a couple of podiums already but I wanted one for myself, but I never had the luck. But finally we did it and it's just fantastic in front of my home crowd.
"I was joking before the race that I'd had a couple of chances before but hadn't had the luck and that maybe this time that would change. And it did. I'm very happy for the fans."
The race's major interest came at the end as Kobayashi battled to hold off Button for the final podium slot. The McLaren driver was half a second behind by the flag, as the Sauber man made up for the team's disappointment after the start in Belgium.
"Fourth definitely isn't a bad result – particularly considering I started from eighth," Button said philosophically. "I ran as high as third during the first stint, but in hindsight it was probably an error to make our first pit stop so early.
"Towards the end, I was able to push and start catching Kamui. But he controlled his final set of tyres very well. I could get close to him, but the only way I was going to get into the DRS zone was by braking extra late into the chicane. And every time I tried I locked up and ran wide. We just didn't have the pace to go for the win today."
Lewis Hamilton had an unhappy race to fifth. Initially he was slowed by debris but said his McLaren "came alive" once it had been cleared in his first pit stop. Later, exiting the pits after his second on the 32nd lap, he made a dramatic pass on Raikkonen in the first corner to cement fifth place ahead of the Finn, who retains his third place in the championship with 157 points to Hamilton's 152.
"I pushed as hard as I could throughout the whole race," Hamilton said. "It was a bit of a struggle in the first stint with a lot of understeer, but after a while the car started turning again. From that moment on it felt really good and I was able to push; but it was too late to have much of an effect on the result. This just wasn't the weekend for me."
Alonso played down the damage to his campaign afterwards, while Vettel refused to talk up his burgeoning chances.
"This time I retire, next time maybe it will be Vettel who will retire," Alonso said. "You never know, this is motorsport. With five races to go it will be like a mini championship."
Vettel said: "It's an important step today but there's still a long way to go."
But as Alonso's job just got a lot harder, Vettel's may have got a lot easier.
FIA Formula 1 Japanese Grand Prix, Suzuka
1 S Vettel (Ger) Red Bull 1hr 28mins 56.242secs
2 F Massa (Br) Ferrari 1:29:16.881
3 K Kobayashi (Japan) Sauber-Ferrari 1:29:20.780
4 J Button (GB) McLaren 1:29:21.340
5 L Hamilton (GB) McLaren 1:29:42.732
6 K Raikkonen (Fin) Lotus F1 Team 1:29:46.666
7 N Hulkenberg (Ger) Force India 1:29:47.401
8 P Maldonado (Ven) Williams 1:29:48.606
9 M Webber (Aus) Red Bull 1:29:50.917
10 D Ricciardo (Aus) Scuderia Toro Rosso 1:30:03.161
11 M Schumacher (Ger) Mercedes GP 1:30:04.011
12 P di Resta (GB) Force India 1:30:19.702
13 J-E Vergne (Fr) Scuderia Toro Rosso 1:30:24.887
14 B Senna (Br) Williams 1:30:24.951
15 H Kovalainen (Fin) Caterham at 1 Lap
16 T Glock (Ger) Marussia at 1 Lap
17 V Petrov (Rus) Caterham at 1 Lap
18 P de la Rosa (Sp) HRT-F1 at 1 Lap
19 R Grosjean (Fr) Lotus F1 Team at 2 Laps
20 C Pic (Fr) Marussia 37 Laps completed
21 N Karthikeyan (India) HRT-F1 32 Laps completed
22 S Perez (Mex) Sauber-Ferrari 18 Laps completed
23 F Alonso (Sp) Ferrari 0 Laps completed
24 N Rosberg (Ger) Mercedes GP 0 Laps completed
1 F Alonso 194pts
2 S Vettel 190
3 K Raikkonen 157
4 L Hamilton 152
5 M Webber 134
6 J Button 131
7 N Rosberg 93
8 R Grosjean 82
9 F Massa 69
10 S Perez 66
11 K Kobayashi 50
12 P di Resta 44
13 M Schumacher 43
14 N Hulkenberg 37
15 P Maldonado 33
16 B Senna 25
17 J-E Vergne 8
18 D Ricciardo 7
19 T Glock 0
20 H Kovalainen 0
21 V Petrov 0
22 J d’Ambrosio 0
23 C Pic 0
24 N Karthikeyan 0
1 Red Bull 324pts
2 McLaren 283
3 Ferrari 263
4 Lotus F1 Team 239
5 Mercedes GP 136
6 Sauber-Ferrari 1 16
7 Force India 81
8 Williams 58
9 Scuderia Toro Rosso 15
10 Marussia 0
11 Caterham 0
12 HRT-F1 0