Rooney returned to training for the Red Devils on Tuesday after missing Saturday's 4-0 win at Newcastle United with a bruised toe.
While there are doubts over whether the striker will play at the Allianz Arena tomorrow night, Moyes is confident that he will be able to feature.
"We'll do everything we possibly can," the Scot told reporters. "He's happy to take an injection to play in the game, which shows you his feeling about the game and about the club.
"We think it's okay. We wouldn't do anything medically wrong. We've taken advice from the doctors and the people who advise us. Everybody knows the type of character Wayne is and he is determined to play. If he is determined we would be mad not to give him that opportunity."
United travel to Germany having drawn last week's first leg 1-1 at Old Trafford.