The 28-year-old forward was initially a major doubt for the clash on Wednesday evening with a toe injury but, after missing United's 4-0 win over Newcastle on Saturday, the striker is in line to return for the second leg in Germany.
Meanwhile, Bayern coach Pep Guardiola is convinced the England international, along with Antonio Valencia, will feature against his side.
"He [Rooney] is going to play. 100 percent," said the Spaniard. "He is going to play I bet you a big big glass of beer. I believe he is going to play, and Valencia too. Rooney is going to play. He is a big player."
David Moyes' men head into the fixture at the Allianz Arena having secured a 1-1 draw in the first leg and the Scot is also boosted by the return of three other senior players.
Ashley Young, Patrice Evra and Jonny Evans all joined Rooney in training on Tuesday, while Ryan Giggs, who missed the win over Newcastle, also took part. Marouane Fellaini and Rafael both missed Tuesday's session.
Bayern, meanwhile, has a number of squad concerns of its own, with Bastian Schweinsteiger and Javi Martinez suspended and Xherdan Shaqiri injured.