The Black Queens beat Group B leaders Cameroon 1-0 on Saturday but failed progress at the 2014 African Women’s Championship on goal difference.
This is the second consecutive time Ghana have suffered a first round exit in the history of the tournament after finishing third between Equatorial Guinea and Cameroon at the 2010 finals in South Africa.
Midfielder Elizabeth Cudjoe scored on 52 minutes for the Queens win which moved them to four points alongside South Africa.
But the Bayana Bayana picked up the other qualification spot in the pool thanks to a comprehensive 5-1 win over Algeria.
Cameroon had already qualified after beating South Africa and Algeria.