Ronaldo was introduced off the bench in the 51st minute with Portugal down 1-0, but the 37-year-old couldn't inspire a fight-back as Morocco became the first African side to reach a semifinal at the World Cup.
Santos also named Ronaldo, who was seen leaving the field in tears at the end of the match, as a substitute for their 6-1 win over Switzerland in the round of 16 and said the result was enough to convince him to keep the same team for the quarterfinal.
"I don't think so, no regrets," Santos said. "I think this was a team which played very well against Switzerland. Cristiano Ronaldo is a great player, he came in when we thought it was necessary, so no regrets.
"If we take two persons that were the most upset it is Cristiano Ronaldo and myself. Of course we are upset, but that is part of the job of the coach and the player."
Portugal only managed three shots on target as they went in search of an equaliser, and afterward Bruno Fernandes was highly critical of Argentinian referee Facundo Tello.
"I don't know if they're going to give the cup to Argentina," Fernandes said. "I don't care, I'm going to say what I think and screw them. It's very strange that a referee from a team that's still in the cup officiates us. They've clearly tilted the field against us."
Fernandes' teammate Pepe also questioned Tello's performance and suggested Lionel Messi's criticism of the referee during Argentina's penalty shootout victory over the Netherlands on Friday had played a part.
"We dominated the game 100 percent of the time," Pepe said. "I think what the referee did today; this is an Argentinian referee. After what Messi said yesterday it seems there's something very weird. We couldn't play in the second half because the referee kept stopping the game.
"I'm very angry, very angry because the referee didn't let us play."
Asked afterward about Tello, Santos played down his impact on the result while also leaving his future as Portugal boss up in the air.
"I think we could have done more and we failed to do so, so I don't think we should blame the referee," Santos said. "I reiterate what I said before the competition, I have a discussion with the president and when we go back to Portugal we will deal with the issue of my contract."