With no VAR or goal-line technology in place to review the incident, Makkelie waved play on much to the dismay of Ronaldo and his teammates.
"As per FIFA's policies, all I can say is that I apologised to the national coach, Mr. Fernando Santos, and to the Portuguese team for what happened," Makkelie told A Bola.
"As a referee team, we always work hard to make good decisions. When we are in the news in this manner, it doesn't make us happy at all."
The reason Cristiano Ronaldo was so angry 👀 pic.twitter.com/8Wua9iNRSx— ESPN FC (@ESPNFC) March 28, 2021
Portugal coach Fernando Santos had revealed Makkelie immediately apologised to him after the game and admitted that he "was ashamed" of the blunder.
After storming off the pitch and throwing his captain's armband on the floor when being denied his first goal in the qualifying campaign, Ronaldo expressed his frustration on Instagram.
"There are moments which are tough to digest especially when we feel the entire nation is being punished," he wrote. "We will keep our heads up and move on to the next challenge."
Speaking at a news conference on Monday, Portugal midfielder Ruben Neves called Ronaldo an "exemplary captain" and said he does not need to apologise to his teammates for his show of frustration at the end of the match.
Asked if Ronaldo had apologised to the squad after the episode, Neves said: "Of course, he didn't apologise. He doesn't have to apologise. Ronaldo is an exemplary player and captain. I think we all feel a little bit of the frustration he felt at that moment; it was a difficult time for us. Everyone knows Cristiano well. We know him well and we know what he can give us every day."
Portugal boss Santos insisted Ronaldo's reaction was down to exasperation and says the player will continue to captain Portugal.
"He will keep it [captain's armband]," Santos said. "Had he offended the coach, his colleagues or the federation, then we would have had to think about it. Nothing like that happened. What happened was a moment of great frustration that could have happened to me. Frustration of someone who always wants to win, who gives everything for the national team. He wrote a post [on Instagram] 10 minutes after.
"Nobody says it [reaction] was beautiful but to question whether he'll be the captain? He was the first to recognise that he shouldn't have done it.
"He is a great example to everyone; he has always been and will continue to be. "It was a moment, a moment of frustration that's all."
Ronaldo and Portugal are back in action on Tuesday when they travel to Luxembourg for their Group A World Cup qualifier.