Rooney was rated doubtful for the UEFA Champions League quarter-final, second leg clash at the Allianz Arena after suffering a toe injury during the first meeting at Old Trafford last week.
He missed Saturday's Premier League win at Newcastle as a result but took a full part in training before the United squad flew out to Germany.
Moyes, whose side drew 1-1 with the defending champions in the first leg, is desperate to have Rooney available for the crucial game, especially as Robin van Persie is already out through injury and January signing Juan Mata is ineligible to play.
"He will definitely play," said Moyes. "We will do all we can to get him on the pitch. He hasn't trained the whole week, but he's willing to have an injection before the game.
"We haven't done anything wrong medically. He's a character. If he's determined to play, we'll let him."
Rooney took to social media to reveal he had suffered no reaction during the morning work-out at Carrington before joining the squad on the plane to Germany.
"Good training session with the lads ahead of the Bayern Munich match," he wrote on his Facebook page.
"It's a massive game for us against a top side but we'll be going in confident and looking to progress into the semi-finals."
Bayern boss Pep Guardiola is also convinced that United will throw Rooney into the action for such an important game.
"He is going to play. 100 per cent. He is going to play I bet you a big, big glass of beer," said Guardiola.
"I believe he is going to play, and Valencia too. Rooney is going to play. He is a big player."
Meanwhile, Moyes admits every player will need to be at their best against Bayern and that his team need to improve from their first-leg performance in order to reach the semi-finals.
"It is the hardest game for us so far. Both teams have top players," he said.
"We can and will play better than in the first leg and we have to play better in order to progress.
"We will need a good performance from everyone. We cannot have any passengers.
"My focus is on getting through. The players are ready and focused and we are relishing it.
"It's a massive game. It's the sort of game United have been involved in over the years, we are ready for it again."
Moyes has drawn some encouragement from Bayern's poor home record against English teams, having failed to win any of their last four games against Manchester City, Arsenal (twice) and Chelsea at the Allianz Arena.
"I think that would be something which is more in Bayern's mind," he said.
"They will have that doubt in their mind. They are European champions but they will have the games they have played against English teams in mind. And we will try to use it to our advantage."
Watch Bayern Munich v Manchester United on Sky Sports 1HD from 7pm on Wednesday