The Italian, who leads by 38 points from Spaniard Jorge Lorenzo, needs only to finish in the top four in Sunday's race to successfully defend his championship.
Rossi, a seven-times winner in the class at the 5.54km Sepang circuit, posted a lap of 2:00.518 seconds, more than half a second faster than nearest challenger Lorenzo, who clocked 2:01.087 seconds.
Honda rider Dani Pedrosa of Spain secured a front-row spot with the third fastest time, relegating Australian Casey Stoner to the second row in fourth position.
Suzuki rider Loris Capirossi of Italy qualified fifth and Spaniard Toni Elias sixth on a Honda.
Earlier in the 125cc category, 16-year-old Spaniard Marc Marquez took his second pole of the season and career ahead of second-placed compatriot Julian Simon, who secured the championship with victory at the Australian Grand Prix last Sunday.










