Large Medium Small |
The Honda rider, lying second in the world championship standings behind team mate Nicky Hayden, was doubtful for the race after falling during Friday's practice and suffering a deep gash under his right knee and a bruised big toe.
The rookie MotoGP rider was cleared by medical staff to take part but he clocked two minutes, 06.612 seconds over the 5.548-km track, the slowest of the 19 riders.
Italian world champion Valentino Rossi, third in the standings, set a Sepang Circuit record of 2:00.61 on his Yamaha to top the time sheets.
American Hayden was second-fastest on 2:01.04 with Italian Loris Capirossi, on a Ducati, third on 2:01.17. Final qualifying takes place later on Saturday.
American Kenny Roberts Jnr. was fourth-quickest with a time of 2:01.90.