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 workout 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."
Rooney, 28, suffered a toe injury in the first leg against Bayern.
Initial reports referred to bruising but there have been unconfirmed suggestions that the player might even have chipped a bone in his foot.
Rooney, however, appeared to have no adverse reaction to the injury and he seemed in good spirits during training.
Defender Rafael, who has been out with a hamstring injury, did not feature.
Midfielder Marouane Fellaini, who complained of feeling dizzy during the 4-0 Barclays Premier League win at St James' Park, was another absentee.
Jonny Evans, returning from a calf injury, was involved fresh from playing for the under-21s on Monday.
Patrice Evra (knee), Ryan Giggs (groin) and Ashley Young (hand) also took part despite injury concerns.
Juan Mata, who did train, misses the game through ineligibility while Robin van Persie is also out with a knee injury.
The odds remain against United as they take on the European champions, despite their creditable performance in the first leg.
Yet for Rooney, confidence that United can not only triumph but go on to win the competition, is still high.
The England forward told UEFA.com: "Of course (I believe we can win it).
"Everyone has their favourites every year - the likes of Barcelona and Bayern Munich - but it does not always happen.
"When Chelsea won it they nearly went out of the competition three times.
"We believe we can go through. We have good enough players.
"It will be tough because in my opinion Bayern and Barcelona are the two best teams left in the competition, so we have to be at our best.
"We are ready. It's an exciting game for us all - the players and the fans - and it's a massive game to be involved in."
After the training session concluded, Rooney said he was feeling good about Wednesday night's second leg.
He wrote on his facebook page: "Good training session with the lads ahead of the Bayern Munich match tomorrow night.
"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."