Schweinstiger picked up his second yellow card of the game at Old Trafford for a lunge on Rooney - however the Bayern boss Pep Guardiola later accused the England striker of successfully conning the referee.
That means the German international will be suspended for the second leg at the Allianz Arena next week - however Rooney insists he wasn't looking to get his opponent sent off, but was instead doing his best to 'stop myself getting hurt.
"I don't really want to say what he said but I think it's a foul," the Manchester United man said.
"It could have gone either 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 sent off and I didn't try to get him sent off.
"The referee has made a decision. I've tried to stop myself getting hurt and the referee has had a decision to make."
A second-half header from Nemanja Vidic gave Manchester United the lead at Old Trafford on Tuesday, only for Schweinsteiger to level things up with an equaliser nine minutes later.
Rooney concedes that Manchester United face a tough task in going to the Allianz Arena to get a result, but believes that Guardiola's team do have a weakness that is open to be exploited.
"They are favourites for the tournament and it will be a tough ask but we needed to give ourselves a chance and we have done that. We have to go and score and [we are] disappointed to have conceded but we defended really well as a team and probably had the better chances and [are] probably disappointed we didn't win."
"They play a high line and with a little more composure we can exploit that," he added.