“We've done a lot of laps today and will now work on tomorrow,” Webber said. “The track is a special one and in terms of difficulty, it's right up there. We have to be very accurate and if you're not, then you get penalized.”
Lotus driver Kimi Raikkonen, who had a mid-session spin, was fourth fastest, followed by teammate Romain Grosjean.
Mercedes driver Lewis Hamilton, who was fastest in the morning session, was sixth ahead of Toro Rosso's Daniel Ricciardo. Ferrari's Felipe Massa was eighth while McLaren driver Jenson Button, who won the Japanese GP in 2011, was ninth.
There were numerous incidents in the afternoon practice.
Alonso lost control of his Ferrari at the Degner curve and finished 10th. McLaren driver Sergio Perez spun off the track and slammed into a tire wall sideways but could be heard over the team radio saying he was fine, and finished 16th.
Williams driver Pastor Maldonado also hit the tires just 12 minutes into the session.
Jules Bianchi sat out the afternoon practice after running off the track early in the first practice and colliding head-on into a tire wall. The Marussia driver was unhurt but was unable to take part in the afternoon session as his chassis was not repaired in sufficient time.