Vettel set a time of one minute 33.852, ending the day a tenth quicker than Webber with Nico Rosberg in the Mercedes less than a tenth of a second further adrift in third.
“The car works fine at the moment, but we need to make sure we set it up the right way,” Vettel, who could win his fourth title tomorrow, said. “It’s good to see we are up there, but it’s not always so important; we need to step up our game for tomorrow, as Mercedes will be strong in qualifying.”
Behind the top three, Kimi Raikkonen set the fourth fastest time, although the Finn had to call it a day with over half an hour of the second session still to run after he made a mistake on his long run, the former World Champion spinning into the gravel trap on the outside of the Dunlop curve and beaching his Lotus.
The day also saw several incidents and crashes as drivers attempted to master the challenging Suzuka circuit. Jules Bianchi managed only eight laps over the course of the two sessions after damage to his Marussia.
Pastor Maldonado was also pitched into the barriers in the first session after a wheel fell off his Williams while in the second session the Venezuelan went off after a mistake at the Degner corner.