The England forward, who missed the Newcastle match and was rumored to be absent for the trip to Germany, trained with the team on Tuesday morning.
Rooney was suffering from a bruised toe, which occurred in the first leg of the quarterfinal tie.
There is no definitive answer from the English side about Rooney’s status, but Bayern manager Pep Guardiola has no doubts.
“He will play, I am 100% sure and I am willing to bet a large glass of beer on it,” he said.
“This is one of the best players I’ve seen and the big players do not want to miss this type of game.”
United are expected to take a similar approach to Germany as they did in the home leg.
Bayern will have plenty of the ball, as they always do, so David Moyes will be comfortable in his negative style looking to hit on the counterattack.
Guardiola’s side is coming off their first loss in 53 games in the Bundesliga, though the league has been clinched for some time.
United’s Rafael and Marouane Fellaini were absent from training.