The 41-year-old superstar said Wednesday he had left the team after coach Jorge Jesus said Ronaldo would not start against Denmark in the Nations League, a match Portugal won 4-2 without him.
Former Real Madrid and Manchester United attacker Ronaldo's future with the national team, for whom he is the leading goalscorer and most capped player, is in doubt after his walkout.
"Regarding Cristiano, I had a conversation with him, and what I told him, and what I repeat here, is this - the most important thing is that, regardless of what happens, Cristiano Ronaldo will never cease to be the greatest symbol of our national team, of our football, and of the country, for what he has done not only in Portugal but throughout the world," Fernandes told reporters Saturday.
Manchester United midfielder Fernandes called for unity after a tumultuous few days in which Portugal fans' opinions have been split over Ronaldo's decision.
"He has a reserved place not only among the best of all time, but also in the hearts of all Portuguese people, and the most important thing is that we stop dividing things," said Fernandes.
"There are no divisions in the national team, it is one and will remain so, despite any noise that may come from outside...
"We are outside of this controversy, but what I ask is that the country does not divide itself, does not make choices, that it respects all sides, but, at the same time, Cris is and will be the biggest icon of our national team, he deserves everyone's respect, regardless of who likes him more or (who likes him) less."
Portugal beat Norway and Denmark away from home without Ronaldo starting and face Norway again on Sunday.
Coach Jesus said Ronaldo was a "symbol of Portugal" and said there would be time to speak about him after Sunday's game in Porto.
"I'm going to focus on the team, on the opponent, which is Norway, one of the five best teams in Europe. That's the problem right now," said the 72-year-old coach.