Portugal were heavy favourites for the friendly contest in Estoril despite naming a vastly different side from the one that defeated Serbia 2-1 in Euro 2016 qualifying on Sunday.
However, it was the African nation that triumphed, as a fortuitous goal from birthday boy Odair Fortes and Gege's close-range effort sank the hosts, who had Andre Pinto sent off on the hour.
Santos believes, however, that Portugal were unfortunate to be on the losing side.
"There were some positive things. The team's attitude in the second half was strong," he said.
"We did very well. Even with 10 men we continued to attack. They did not get to our goal.
"The attitude of those who were in the field and those who came off the bench was good. We could have reduced the result."
Santos admitted that his side were not at their best during the opening period.
He added: "In the first half there were negative aspects of positive people. We lacked some aggression and there was a 10-minute period where we lacked concentration."
