The England forward is United's main fitness concern ahead of the potentially season-defining clash at the Allianz Arena after missing Saturday's 4-0 win at Newcastle with a toe injury.
Rooney was involved as the United squad underwent a light workout in a session partly open to media at their Carrington training base before flying out to Germany.
United fought out a 1-1 draw with Bayern in the home leg at Old Trafford.
At Bayern's pre-match press conference in Munich, manager Pep Guardiola was in no doubt that Rooney would line up for the Reds on Wednesday night.
He said: "Rooney is going to play, 100%. He is going to play, I bet you a big, big glass of beer."
Guardiola described Rooney as "a big player, one of the best I have seen in my career".
Defender Rafael da Silva, who has been out with a hamstring injury, did not feature and midfielder Marouane Fellaini was another absentee after complaining of dizziness during the weekend win at St James' Park.
Jonny Evans, returning from a calf injury, was involved fresh from playing for the under-21s on Monday.