Ronaldo left the squad ahead of Portugal's Nations League meeting with Denmark after coach Jorge Jesus indicated he would not start the match. Portugal went on to win 4-2 in Copenhagen, maintaining their perfect start to Group A4.
The 41-year-old subsequently said he would reveal the reasons behind his decision to leave the camp "in due course", leaving his international future uncertain.
Fernandes, who has played alongside Ronaldo for both club and country, said the situation should not overshadow Portugal's campaign.
"I had a conversation with Cris, and what I told him, and what I repeat here, 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," Fernandes said.
"He has a reserved place not only among the best of all time, but also in the hearts of all Portuguese people."
Fernandes also urged supporters not to take sides as speculation continues over the dispute.
"There are no divisions in the national team. It is one and will remain so, despite any noise that may come from outside," he added.
"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."
Ronaldo remains Portugal's record goalscorer and most-capped player, with 146 goals in 234 appearances. He has also helped the country win Euro 2016 and the Nations League twice.
His latest absence came after he was an unused substitute in Portugal's 2-1 win away to Norway. Jesus had previously selected him for the opening Nations League victory over Wales, but Ronaldo played only 67 minutes before being left out of the starting line-up for the following match.
Jesus, who previously managed Ronaldo at Al Nassr, echoed Fernandes' assessment of his former player while attempting to shift attention towards Sunday's clash with Norway in Porto.
"Ronaldo is a symbol of the national team and of Portugal. After the game, there is plenty of time to talk about that," Jesus said.
"I'm going to focus on the team, on the opponent which is Norway. That's the problem right now."
Portugal sit top of Group A4 with nine points from three matches and will look to continue their perfect record against Norway.
Fernandes believes the squad must remain focused on that objective while allowing the wider Ronaldo situation to be resolved away from the team.
"All parties should resolve their issues behind closed doors," he said. "I think that's how it will be, and that everything will end well on both sides."