The German, who will wrap up the championship if he wins on Sunday and Ferrari's Fernando Alonso fails to finish in the top eight, lapped with a best time of one minute 33.852 seconds in an afternoon session with plenty of incidents.
"The car balance is decent, but I think we can still improve," said the Red Bull driver, who had been third and behind the two Mercedes drivers in a morning session led by Lewis Hamilton.
"It's good to see we are up there, but it's not always so important; we need to step up our game, as Mercedes will be strong in qualifying."
Alonso, 77 points adrift of the German with five races remaining, ended the day with sixth and 10th places on the two timesheets.
"We were not as competitive as we wanted to be and now we must try and improve, putting together a series of changes that we already have in mind," he said.
As the Spaniard got out of the car and removed his helmet at the end of the second session, he was shocked to be told of the death in Spain of compatriot and former Marussia test driver Maria de Villota.
The news left the Suzuka paddock mourning a friend, with emotional tributes to a woman who had remained passionate about the sport despite losing an eye in a life-threatening test accident last year.
While Vettel took up his familiar place at the top of the timesheets, others hit trouble.
Lotus's Kimi Raikkonen, Pastor Maldonado for Williams and McLaren's Sergio Perez all went off in the afternoon.


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