Although the pair have long since made up, Ronaldo's infamous wink as Rooney saw red in Gelsenkirchen remains one of the abiding memories of Germany 2006. Rooney insists he did not mean to stamp on Portuguese defender Ricardo Carvalho.
But the incident left England to complete the quarter-final with only ten men, the effort to reach the final whistle counting for nothing as Sven-Goran Eriksson's men lost on penalties. Three years on, a much less abrasive 23-year-old will take on Ukraine on Saturday knowing England's place in South Africa is secure.
The same cannot be said of Ronaldo, who is battling to be fit for a double-header with Hungary and Malta which, even if they are successful, could end with arguably the world's number one player missing out on an appearance on the greatest stage, just as Rooney did when England failed to qualify for UEFA EURO 2008.
"It would be nice to see Portugal not there because they have knocked us out of the last two tournaments," reflected Rooney. "Obviously when we didn't qualify for Euro 2008, we got a lot of stick. You have banter with your team-mates. But it's important not to go too far because it is an important issue and, to be honest, I am not too bothered whether they are there or not."
It is to Rooney's credit there is no malice behind his words, just a professional attitude and the prospect of having a bit of fun at Ronaldo's expense. In fact, just because the Portugal superstar has left for Real Madrid, Rooney has not changed his opinion that Ronaldo is the world's number one, even defending his old team-mate against the accusation that he did not care enough about the team - a trait which led to Ferguson playing the England star out of position.
"It is clear for everyone," said Rooney. "Ronaldo is definitely the best player. He scores goals and I have watched his first few games for Madrid and he seems to have improved again. He is even passing the ball a lot more!
"At United, people said he didn't run back. But look at what he did going forward. As a team we realised that if he was as good as that going forward, we had to make up for it by going back. That is what happened and we were very successful, so you can't argue."
Maybe Ronaldo does not deserve such warm words given the stigma of his wink will never quite go away, on English shores at any rate. Yet the winger has also left a template for Rooney to follow. There was a time when the Merseysider was rated the better of the two. Then Ronaldo streaked clear.
Now the gap is closing, with Rooney's position at the head of the FIFA World Cup goalscoring charts in Europe the tangible proof. "I hope I can take my game to the next level as well," he said. "Physically, Ronaldo improved a lot over the last three years. He worked hard in the gym and got a lot tougher. I am still trying to improve most areas of my game, especially my link-up play, goalscoring and heading. I should score more often with my head."
Rooney has been around for so long it is easy to forget he is still not quite 24. He has a FIFA World Cup campaign behind him, as well as that explosive contribution he made to UEFA EURO 2004. On both occasions, those dreaded broken metatarsals undermined him, breaking one in Portugal and struggling to recover from one before Germany.
This time round he is hoping for good fortune on the fitness front because finally, under Fabio Capello, he has found someone prepared to trust him in the role which suits him the most, constantly changing positions with Steven Gerrard. "It is the perfect role for me and it is working really well," he said. "I just hope this time I can stay fit and do all the training beforehand. That will make a big difference.
"Football is different for me now. I think about the game a lot more. At 16 there is no fear whatsoever - you just play and enjoy it. But the more games (you play) you wonder about what is going to happen if you win or lose."