The Super Eagles of Nigeria were held to a goalless draw by the Black Stars in Kumasi last week, only to play another 1-1 draw at Abuja, Nigeria.
These results means that Nigeria will not be at the 2022 World Cup.
In the second leg played at the Moshood Abiola Stadium, the visitors took the lead through Thomas Partey.
The Arsenal midfielder placed a long range shot under Francis Uzoho to give Ghana the lead.
Nigeria equalized, after VAR awarded a penalty for a foul on Ademola Lookman. Captain William Troost-Ekong stepped up to make it 1-1.
The Black Stars qualified on away goals.