Reigning champion Casey Stoner lapped under two minutes on the final day's testing in Malaysia.
The Australian, who missed the opening day with a back problem, managed a best time of one minute 59.607 seconds.
"It's been a good test. We only managed two out of three days but the weather has been good to us and we've been able to do what we planned."
Honda team-mate Dani Pedrosa was third, with Britain's Cal Crutchlow seventh.