Saki Hayashi scored 23 points as the Asians outclassed the D’Tigress.
Yuki Miyazwa added 19 points for the hosts, bringing it up to a total of 19 3-pointers in the game.
Tokyo Olympics: Minister of Sports, Dare reacts as D’Tigress lose to USA
Japan were up 30-22 after the first quarter, but Nigeria cut its deficit to 38-36 before Japan scored 13 straight points to take control.
Japan led 51-38 at half time and didn’t take off their foot off the pedal in the second half as the West Africans failed to get back in the game.
Nigeria (0-3) became the latest African country to not win a game in the Olympics.
They were the last team from the continent to be victorious in the Olympics when that team went 1-5 in the 2004 Athens Games.