Pedro Neto gave the hosts the lead before Akor Adams equalised for the Super Eagles.
Francisco Conceiçao scored the winner in the 74th minute to send Portugal into the World Cup with a win.
Ronaldo led the line for Portugal, but was hugely disappointing, and Martinez emphasised that his starting lineup remains fluid as Portugal prepare for their World Cup opener against DR Congo on June 17.
“I keep emphasizing that I am very selective,” Martinez said, according to OJogo.
“There is no fixed starting XI. In contemporary football, 26 players can contribute… It would be erroneous to assume that I have a starting XI, only to discover in four or five days that other players are in better form.
“I cannot restrict talent to just 11 players. That is a mistake I refuse to make.”
Ronaldo, 41, remains a polarising figure among fans, with some believing he is way past his best.
However, all signs point to the Al Nassr man starting Portugal’s opener against DR Congo.