Nora Hauptle’s side suffered their first defeat in the calendar year with the Namibians pipping Ghana to get a victory.
The home side's first-half lead was enough to secure the win but could not get them through to the tournament which will be hosted in Morocco.
Namibia were the better side. They controlled the game and limited Ghana's threat to become the first team to prevent the Black Queens from scoring in eleven games.
The defeat is also their first under new manager Nora Hauptle.
However, they have achieved the ultimate goal of qualifying for the WAFCON for the first time since 2018.
Ghana have become the fourth country to secure qualification joining the host nation Morocco, South Africa, and Algeria.
