The deportees – 95 males and two females – arrived at Murtala Muhammed International Airport from Johannesburg on Monday night.
Those accused of criminal offences were handed over to the police for prosecution, while those accused of committing civil offences were allowed to go home.
This is coming in the wake of xenophobic attack on Nigerians in South Africa and their businesses in the country.
The Nigerian government condemned the attacks, and also threatened consequences if they are not checked.
The Nigerian senate has also resolved to send a strong delegation to the country to protest against the attacks.
In the space of a month, about 500 Nigerians have been deported from different countries.
Last week, 314 Nigerians were forced to return home as a result of harrowing experiences in Libya.
On Monday, 41 Nigerians girls who were trafficked to Mali returned.
The economic situation in the country has made many consider the other option of seeking green pasture abroad.