The England forward is United's main fitness concern ahead of the potentially season-defining clash at the Allianz Arena after missing Saturday's win at Newcastle with a foot injury.
Rooney was involved as the United squad underwent a light work-out in a session partly open to media at their Aon Training Complex 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 per cent. 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".