The 26-year-old Yamaha rider rode a brilliant race from pole position, holding off Marquez for 22 laps at the Motegi Twin Ring track and frustrating his fellow Spaniard's championship ambitions for the second week in a row.
Honda rider Marquez, 20, still leads the championship by 13 points, however, and a fourth place finish at Valencia on November 10 would guarantee he becomes the youngest champion in the 64 years of the premier class of grand prix racing.
Marquez's 17-year-old brother Alex earlier won the Moto3 race for his first grand prix victory in an action-packed encounter that also kept that title race alive, while Pol Espargaro's victory in the Moto2 race sealed the championship for the Spaniard.
(Writing by Nick Mulvenney; Editing by John O'Brien)
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