
Ferrari dominated the first practice session in the morning on the new Fuji Speedway but Hamilton turned the tables in the afternoon, as he clocked a time of one minute 18.734 seconds for the 4.563- kilometre circuit.
Hamilton's McLaren team-mate Fernando Alonso was second fastest with a time of 1:18.948,followed by Ferrari's Felipe Massa and Jarno Trulli in a Toyota.
Ferrari's Kimi Raikkonen was fifth, nearly a second slower than Hamilton, but the Finn did register the fastest time in the morning session with a lap time of 1:19.119 minutes.
His Brazilian team-mate Massa was 0.379 seconds slower to come in second, followed by the McLarens of world champion Alonso and Hamilton.
Hamilton leads Alonso by two points in the overall standings with just three races remaining. Raikkonen lies third, 13 points behind the Briton.
Ferrari are already assured of their 15th constructors' title after closest rivals McLaren were docked all their points in the wake of the spying affair.
DPA