United are in desperate need of Rooney's power and finishing ability in Munich as they look to improve on a 1-1 home draw in the first leg of their Champions League quarter-final last week and book a spot in the last four.
"He will definitely play," Moyes told reporters. "We will do all we can to get him on the pitch. He is happy to take an injection.
"It is the hardest game for us so far. Both teams have top players."
Moyes said every player would need to be at their best and that his team needed to improve from their first-leg performance in order to edge past last season's treble winners into the semi-finals.
"We can and will play better than in the first leg and we have to play better in order to progress," said Moyes. "We will need a good performance from everyone. We cannot have any passengers," Moyes said.
United were all but written off before the first leg against the powerful Bavarians, but have given themselves a chance with the draw at Old Trafford.
Bayern slumped to their first league defeat in 53 games on Saturday and have gone three games without a win for the first time since 2011.
Another worry for Bayern is their failure to win any of their last four matches against English opposition at the Allianz Arena, a run that started with their penalty shootout defeat to Chelsea in the 2012 Champions League final.
They have since lost and drawn against Arsenal and lost to Manchester City.
United's own recent form, on the other hand, with four goals in each of their last two Premier League wins, is another encouraging sign for Moyes.
"My focus is on getting through," said Moyes. "The players are ready and focused and we are relishing it."
Defender Rafael (thigh) and midfielder Marouane Fellaini, who complained of feeling dizzy during the 4-0 Barclays Premier League win at Newcastle, were absent from United's final training session.
Patrice Evra (knee), Ryan Giggs (hamstring) and Ashley Young (hand) took part despite their injury concerns. Midfielder Juan Mata (cup-tied) and striker Robin van Persie (knee) are unavailable.
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