Rooney received his marching orders in the 62nd minute after treading Ricardo Carvalho.
Referee Horacio Elizondo was set to give only a foul but Ronaldo's protest seemed to convince the Argentinean official to hand Rooney a straight red card.
Rooney told The Sunday Mirror that his Manchester United mate called him before the game and said "I'll get you sent off."
Rooney, who pushed Ronaldo on his was out as England went on to lose on penalties after a goalless draw, said he won't be playing alongside the Portuguese again.
But Ronaldo refused such accusations saying that Rooney is his friend and he couldn't have wanted him to be red-carded.
"I complained to the referee about the foul but I didn't ask him to red card Rooney," Ronaldo was quoted as saying by Sky Sports Network.
FIFA announced they will undergo an investigation about the whole incident and Ronaldo will be one of the players to be questioned.