Jockey Christophe Soumillon placed Epiphaneia alongside Satono Shuren and Tamamo Best Play for the majority of the 2400-metre weight-for-age race and when the field turned for home at Tokyo Racecourse, no horse managed to stick with the four-year-old.
Epiphaneia unleashed a blistering burst of speed to win comfortably from Just A Way and Spielberg.
Gentildonna, who was aiming for a third straight Japan Cup victory, never made a serious push for victory but produced a decent late run to claim fourth.
But it was the Katsuhiko Sumii-trained Epiphaneia who took out the 34th-running of the $5.8million race.