The German international and his manager Pep Guardiola were seen making diving gestures following the incident, but Rooney insists that he was fouled.
"I don't really want to say what [Schweinsteiger] said, but I thought it was a foul," Rooney told reporters. "If I didn't get out of the way he could have hurt me, he's gone in with his studs and the referee has booked him, so it's not my decision.
"It's not nice to see anyone get sent off. I didn't try and get him sent off, the referee has made the decision. I have tried to stop myself from getting hurt and the referee has had a decision to make.
"He's a great player and he's obviously someone they will miss - and [Javi] Martinez as well being suspended - but they have a great squad of players who can come in."
Rooney went on to admit that Bayern are the favourites to progress ahead of next week's quarter-final second leg in Germany.