Vettel used a two-pit-stop plan while other favorites, including pole-sitter Mark Webber, stopped three times in the 53-lap race. On lap 42 when Webber stopped for the third time, Vettel took the lead and never gave it up.
Webber and Vettel, who both drive for Red Bull-Renault, were 1-2 on the grid with Romain Grosjean, in a Lotus-Renault, starting third. Grosjean passed both for the early lead and was nicely in front for the first 30 laps.
His second pit stop allowed Vettel to move up. Webber went ahead for the first time when Vettel pitted but when Webber went into the pits, Vettel took the lead for good.
Vettel finished the 191-mile race at the Suzuka Circuit in 1 hour, 26 minutes, 49.3 seconds. Webber ended up second 7.1 seconds back and Grosjean came in third, 9.9 seconds back of Vettel.
It was the fifth consecutive Formula 1 win for Vettel, who has a total of nine wins in 2013. Sunday marked his fourth win at the Japanese Grand Prix, as he also finished first in 2009, '10 and last year.
He has 35 Grand Prix wins in his career, which is fourth most all-time.
Alonso's fourth-place finish kept Vettel from clinching a fourth straight drivers' championship. Vettel has 297 points, just 3 points from locking up the title. Alonso is second with 207 with Raikkonen in third with 177 followed by No. 4 Lewis Hamilton (Mercedes) with 161 and Webber in fifth with 161.
There are four races left on the 2013 Formula 1 calendar with the Oct. 27 Indian Grand Prix next on the schedule.