In the match held at the Estadio Nacional de Brasilia, Ghana defender John Boye scored an own goal in the 31st minute.
Asamoah Gyan equalized the match in the 57th minute.
With 10 minutes remaining, World Player of the Year Cristiano Ronaldo scored the winning goal for Portugal.
The goal gave Portugal a 2-1 win to finish the group with four points, the same as the United States. The US advanced from the group with a superior goal difference.
Germany beat the US and qualified for the last 16 with seven points as the champion of Group G.
On Tuesday, Germany is to play Algeria and the US face Belgium.