In the women's wrestling competition, Blessing Oborududu won a silver medal for Nigeria in the 68kg category, while Ese Brume won a bronze medal in the women's long jump.
Team Nigeria had a poor showing, failing to reach the medal zone in the majority of the games they competed in.
For failing to comply with out-of-competition drug testing procedures, ten of the country's competitors were disqualified.
Blessing Okagbare was also disqualified due to doping. She was unable to compete in the women's 100m and 200m semi-finals.
On the 205-country medal table, the country came in 69th place.
The team landed in Abuja about 1 p.m. on Saturday.
Sunday Dare, Minister of Sports, expressed satisfaction with the team's performance in Tokyo 2020.