The 41-year-old Al-Nassr forward met Jesus on Wednesday in an attempt to address the situation after he was left on the bench for the Nations League victory.
Ronaldo subsequently announced that he had decided to leave the national team.
"After the press conference of the national team, and following a conversation with the President of the Portuguese Football Federation, I have decided to leave the national team," he wrote on Instagram.
"In time, I will tell all the Portuguese the truth about the reasons that motivated me to leave the national team, to which I always devoted myself.
"Now is the time to wish Portugal and all my teammates good luck, without exception."
The decision came shortly after Jesus had addressed the situation in his own press conference.
The Portugal coach said there had been no major incident between himself and Ronaldo, although he acknowledged that the forward was unhappy after spending the match against Norway on the bench.
"There was no incident whatsoever," Jesus said.
"Any player - and I was a player myself - when you spend 20 or 30 minutes warming up and then don't get on, no-one is happy about that."
Jesus explained that he had originally intended to use Ronaldo as a substitute but ultimately decided against bringing him on.
"Afterwards, as coach, I decided not to bring him on. It's nothing to make a fuss about," he said.
He also insisted that Ronaldo's status would not influence his decisions.
"The way I was reading the game (against Norway), he didn't come on," Jesus said.
"Because it's not Cristiano, just like it will never be any player that will change my ideas as the coach. Never! Not him, not anyone in football. Not him, not any president. Never! Zero!"
Goncalo Ramos started against Norway and scored the winning goal, with Jesus subsequently indicating that the AC Milan forward would also start the next match against Denmark.
Ronaldo's departure raises fresh questions about the future of his international career.
He had only recently spoken about his desire to continue representing Portugal, saying he still believed he could help the national team and that he would stop when he felt he could no longer contribute.
"I still believe that I'm able to help the national team to reach what they want, and will finish when I feel like I'm not doing anything here," Ronaldo said previously.
"I think I can give to the national team my support, not only through the goals, but also outside of football."
Ronaldo has won 234 caps for Portugal and scored 146 international goals.
His latest decision comes after his relationship with Jesus came under scrutiny just months after the coach took charge of the national team.
Jesus has maintained that his decision against using Ronaldo from the bench against Norway was purely tactical.
Ronaldo, however, has said he will eventually explain the reasons behind his decision to leave the national team.