Rooney appeared to signal to the official before Kompany was red-carded for a two-footed tackle on Nani in Sunday's explosive FA Cup third-round clash at the Etihad.
But he explained to The Sun: "I didn't wave any imaginary card. I clearly pointed out, and a few other players did as well, that it was a two-footed tackle. It was down to the ref to send him off.
"As professional footballers, when you leave the ground and go in two-footed we've now been told by the referees it's a red card. Refs come and see us before the season starts. I felt Kompany had done that."