One major difference between these two organizations is that one of the is only associated with one continent, while the other is associated with four continents.
The African Union is consisted of members that are exclusively from the African continent. This organization has been established so that the African nations can support each other, develop their economies, remove the trade barriers, easy and free movement of people, technology and ideas.
The Community of Portuguese Language Countries has the same goals as the African Union, but it is not a regional organization, instead it has members from four different continents. Members of this organization are Portugal, Brazil, Mozambique, Angola, Cape Verde, Guinea Bissau, Sao Tome and Principe, and Timor Leste, or we can say that the organization is made out of the former Portuguese colonies.