A profligate Yuki lost the match 6-3 2-6 1-6 in one hour and 46 minutes.
The Indian started brilliantly and took a little over half hour to pocket the opening set but the match turned on its head in the very next set.
The Japanese raised his game, helped by the sudden surge in the number of unforced errors committed by the Indian.
In the end, it was a case of missed opportunities for Yuki, who settled for a third-place finish. In the previous edition of the Games, Somdev Devvarman had won India's maiden men's singles gold.