Makoto Tamada was Japan's last rider to start on pole in 2004.
Nakagami took pole just two days after signing a new multi-year deal with Honda, and he becomes the season's sixth different pole-position rider.
MotoGP star Jason Dupasquier dies after crash
Petronas Yamaha's Franco Morbidelli will start in second, while Suzuki's Alex Rins joins them on the front row. Rins' team mate and championship leader Joan Mir starts well back in 12th position. (Reporting by Rohith Nair in Bengaluru; Editing by Hugh Lawson)
Quartararo sets lap record to take pole at Italian GP
IWD special – 'Any sport should be equal' – FHO Racing boss on proving women belong in motorsport