The German led from pole and triumphed comfortably, despite taking the chequered flag just 0.9 seconds ahead of the Australian, for the second year in a row at Suzuka.
McLaren's [ Images ] world champion Jenson Button [ Images ], one of five title contenders, failed in his gamble of starting on harder tyres than the others and was fourth with team mate Lewis Hamilton [ Images ] fifth.
Webber now has 220 points to 206 for Alonso and Vettel, with the Spanish double world champion having won four races to the German's three.
Australian Webber was again lucky, losing second place to Renault's [ Images ] Robert Kubica [ Images ] at the start but gaining it back when the Pole came to a halt on lap three with the rear right wheel missing from his car.
"I'm really, really happy and it's about time," said Vettel of his first win since Valencia in June despite starting eight times on pole.
Webber was also pretty pleased.
"A very good day for me," he declared. "It was probably difficult for me to win the race unless I got the start."
Hamilton, who started with a five-place grid penalty on a weekend where nothing went right for him, dropped to fourth overall on 192 points with his hopes fading.
"I was happy that I finished," said the 2008 champion.
"I lost third gear as I was shifting up. It's a tough one for the team. Maybe this is a sign," he added.
Button fell further behind in fifth overall, with 189 points and just three races to try and make up a 31-points deficit if the Briton is to become the first driver since 1957 to win back-to-back titles with different teams.
It was the championship leaders' third one-two finish in 16 races. Red Bull now have 426 points to McLaren's 381 in the constructors' standings.
In an eventful race run in bright sunshine after heavy rain had made the track undriveable on Saturday and forced qualifying to be postponed to Sunday morning, the safety car was deployed for five laps after mayhem at the start.