The young Indian pair failed to counter the agility and decisiveness of the Japanese duo, going down in three straight sets 6-11 6-11 9-11 at the Yokohama Cultural Gymnasium.
Ghosh and Desai earlier became first Indian pair to reach the last-eight stage of a super series event.
In the men's singles, Achantha Sharath Kamal bowed out of the competition after suffering a 0-4 defeat at the hands of Liqin Wang, world number nine from China, later in the day.