Australian Mark Webber, still without a win this year, was fourth for Red Bull, who have 518 points to McLaren's 388 and could wrap up the constructors' championship in South Korea next weekend.
Schumacher, who briefly led the race during the pitstops, was sixth and Massa seventh.
In a race of only one retirement, Mexican Sergio Perez was seventh for Sauber ahead of Renault's Russian Vitaly Petrov.
Germany's Nico Rosberg, who started on the back row after failing to set a lap in qualifying, roared back to take the final point.
Image: Red Bull driver Sebastian Vettel of Germany leads the field into Turn One at the first lap during the Japanese Formula One Grand Prix at the Suzuka Circuit in Suzuka, central Japan, Sunday, Oct. 9, 2011.