"I am sure he was joking," the Portuguese forward told a news conference on Friday.
"He is a good friend of mine and he knows Portugal are a top team. He played a few times against us and never won. But I am sure he was joking as he has friends here (in the Portugal squad)," Ronaldo said.
Earlier on Friday, British newspapers quoted Rooney as saying "it would be nice" to see Portugal not qualify as they had knocked out England in their last two appearances in major tournaments, the 2006 World Cup and Euro 2004.
"When we didn't qualify for Euro 2008, we (the United players) got a lot of stick (from Ronaldo)," Rooney said.
NEWS: Ruthless Rooney hopes Portugal fail to qualify
England have already qualified for next year's finals in South Africa while Portugal are third in Group One and must win both their remaining matches against Hungary and Malta, while hoping Sweden drop points, to reach the playoffs.
Portugal coach Carlos Queiroz, who worked with both players at United, said Rooney was showing his respect for Portugal.
"Knowing him, I know why he said that; it's because it shows his respect for Portuguese football and Ronaldo particularly," Queiroz told the news conference.
Rooney was sent off against Portugal in the 2006 World Cup quarter-final for stamping on Ricardo Carvalho in a match that triggered a media backlash against Ronaldo.
Ronaldo had suggested to the referee that Rooney should be sent off and was seen to wink at his bench when the official did so.
Rooney said he had no doubt that he deserved to be sent off and made clear there were no hard feelings towards Ronaldo, saying the Portuguese had only improved since his move to Real Madrid.
Portugal play Hungary in Lisbon on Saturday and Malta in Guimaraes next Wednesday.
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