First-half efforts from Otavio and Diogo Jota put Portugal in control in World Cup qualifying play-off semi-final, but Burak Yilmaz pulled one back after the hour mark and had a chance to equalise from the penalty spot with five minutes remaining.
However, Yilmaz missed the target from 12 yards and Matheus Nunes completed a 3-1 win for the hosts in stoppage time, with Ronaldo hitting the bar in the final act of the game.
The Manchester United forward had five efforts on goal and hit the target with two of them. Diogo Jota (38), who played 20 minutes fewer than Ronaldo, was Portugal's only outfield starter with fewer touches than him (40).
Ronaldo has scored just four goals in his past 13 appearances in all competitions for club and country, but the Portugal boss is unconcerned by his displays.
"Ronaldo is judged on the goals he scores, it's always that way," said Santos.
"From my perspective, he played a tremendous game, bringing the group together, working and pressing with the intensity of the game.
"He didn't score, but that doesn't invalidate what was an excellent performance for Ronaldo. He had several opportunities. He didn't convert them, but he opened up a lot of spaces for others and that's something to highlight."
Ronaldo is one of several veterans in the side that it has been suggested should be phased out by Santos to make way for a new generation, but the coach spoke out in defence of the more experienced options at his disposal.
"The one that everyone is asking to be replaced is the only golden generation. I'm very sorry to say this, but it is the only one that has brought a trophy to Portugal," he said.
"Now, if you ask me if Portuguese football has a bright future ahead of it, with high-quality players capable of responding at any time, I'd say yes.
"Portugal have always had great players, but the golden generation is the one that won the gold."