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14 years ago today, Rooney was sent off in the quarter final in Germany for stamping on Ricardo Carvalho but his club teammate Ronaldo was accused of influencing the decision of referee Horacio Marcelo Elizondo and getting him the red card.
CR7 was seen winking to the Portugal bench afterwards and his antics angered England fans and members of the press on these shores.
Portugal went on to beat 10-man England on penalties, and it was thought afterwards that a rift between Ronaldo and Rooney, two of United's most influential players, was developing - and there was talk of the former heading for the exit door.
That never happened, as the duo struck up a wonderful understanding in the next three seasons at Old Trafford.
However, Ferguson, who Ronaldo views as a father figure, revealed that the incident 14 years ago played a part in Ronaldo's decision to leave United for Real in 2009, even if Rooney was mature and professional about the whole episode.
In a lengthy interview with France Football, following Ronaldo's fifth Ballon d'Or win in 2017, the legendary manager said: "It actually all started during the 2006 World Cup when Rooney was sent off against Portugal and the press and critics accused Cristiano of having contributed to that. It was unfair.
"But I have to say that on that occasion, Rooney was fantastic and managed the situation very well.
"He came to me and asked if he and Cristiano should do an interview together to silence all the critics before the start of season.
"I told him that the idea did not seem wise. I thought that it was some sort of gimmick, and I do not like gimmicks.
"Through Jorge Mendes, we were informed that Cristiano was unhappy. He told Jorge that he would not come back to United and that he wanted to go to Real Madrid. At the time [Ramon] Calderon was running for Real Madrid's presidency and used Cristiano as a reason to vote for him, which was unseemly of him.
"I took the plane to Lisbon to meet Cristiano in Carlos Queiroz's house. I told him, 'You are not leaving this year. I do not want to sell you to Calderon. But if you play well, you will leave later.' Jorge Mendes was amazing. He did not want Cristiano to leave. He felt that he was not ready.
"He put his financial interests aside as well as those of the player - all that money he could have won - for Cristiano's career, including that amazing 2008-2009 season.
"He knew that I would not go back on my promise. His concentration and work ethic were marvellous. In 2009, Florentino Perez became president of Real, which made it easier for us to work with him concerning his transfer."
Years later Ronaldo would also confirm that the two brushed the incident under the carpet after a chat when they returned to Manchester.
He told Goalhanger: "We are still friends, we speak about that and he understands my point of view. Of course, he helped me in all circumstances.
He said: 'Cristiano, this is the past, let's speak about the present, let's win trophies together'."
Rooney and Ronaldo won three Premier League titles in a row following the spat, as well as the Champions League in 2008.
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