The 28-year-old has been sidelined with a toe injury since the first leg of the Champions League quarter-final, missing the 4-0 league win over Newcastle, but has been winning his battle to be fit.
Rooney returned to training on Tuesday ahead of the Allianz Arena clash, with Pep Guardiola earlier revealing he was convinced the striker will play, and Moyes says United are desperate to include him.
"He'll definitely play. We'll do everything we possibly can [to get him on the pitch]. He's happy to take an injection to play which I think shows you his feeling about the game and the club."
"We wouldn't do anything medically wrong. We take advice from the doctors who advise us. Everybody knows the character Wayne is and he is determined to play. If he is determined we'd be mad not to let him do so."
United head to the Allianz Arena having earned a hard-fought 1-1 draw at Old Trafford seven days ago, but Moyes is keen to have more of a hold on the second leg and expects his squad to improve in Germany.
"I'd like to have more possession and have a bigger effect on the game, and my plans are to do that. But they were also my plans in the first game as well," Moyes continued.
"You have to respect your opponents and on the night they did some good things. But I expect us to play better and I believe we can. To get through, we will have to.
"It's the hardest game for us so far. Both teams have top players. We're almost treating it like a cup final. My focus is on getting through. The players are ready and focused. We're relishing it."