Red Bull's Vettel, who can clinch a fourth successive Formula One world title this weekend, lapped in 1:34.768.
Fernando Alonso, second in the standings behind Vettel, was sixth quickest.
Vettel can become only the third man to win four titles in a row on Sunday if he wins and Ferrari's Alonso fails to finish in the top eight.
The German has won the last four grands prix to open a 77-point lead with only 125 available from the last five races.
Hamilton, who complained Vettel's dominance was becoming boring after his rival's victory at South Korea last weekend, threw his car into Suzuka's high-speed corners, setting fastest lap after fastest lap.
Marussia's Jules Bianchi hit a wall heavily at turn nine early on before Williams driver Pastor Maldonado lost a wheel coming through the sharp "Spoon" curve.
"I lost a wheel," he coolly informed his team over the radio, the bouncing projectile well snaffled by marshals as it headed towards a wall.