The Spurs manager is without 10 first-team players in Germany after resting Harry Kane, Dele Alli, Jan Vertonghen and Serge Aurier.
Six others – Hugo Lloris (elbow), Michel Vorm (calf), Ben Davies (ankle), Harry Winks (ankle), Tanguy Ndombele (groin) and Erik Lamela (hamstring) – remain sidelined.
Youngsters Kyle Walker-Peters, Juan Foyth, Japhet Tanganga, Oliver Skipp, Ryan Sessegnon and Troy Parrott should feature against the Bundesliga giants, while there could be first starts under Mourinho for Victor Wanyama, Christian Eriksen and Giovani Lo Celso.
The Portuguese, who has been in the job for exactly three weeks, admitted he has not had the chance to properly assess many of his squad players and is looking forward to the opportunity at the Allianz Arena.
"I am not having the time to know all my players well, and this is a great opportunity for some of them to play, for some of them to show what they are capable of," Mourinho told a press conference.
"A player in competition is different to a player training. Some of my boys didn't have the chance to play many minutes in these five matches since I arrived.
"We are going to have an incredible number of fixtures until the new year and I think it is understandable that we are going to make a few changes and we are going to rest a few players and give opportunities to other players."
Mourinho has talked up the potential of Spurs' young players since joining the club, having faced criticism for his handling of youth while in charge of Manchester United and during his second spell at Chelsea.
He pointed to United's Scott McTominay and Real Madrid's Raphael Varane as examples of players he has blooded and stressed that developing youngsters is part of Tottenham's DNA.
"Scott McTominay only the best player at Manchester United, Rafael Varane is one of the best players in the world – it’s fair criticism, yeah," Mourinho said sarcastically.
"It’s part of the DNA of the club, part of the culture and also part of the passion and relations between the fans and the team," he added. "The Spurs supporters like to see the young boys coming from the academy, different to some other big clubs in English football and also world football. It’s part of us.
"I had players on the bench [against Burnley on Saturday] like Eriksen, Lo Celso but then opportunities went to the U20s, which I think is very important for them."
Bayern are guaranteed top spot in the group while Spurs will qualify in second, meaning Mourinho's side are playing only for pride and for revenge after Bayern inflicted their biggest-ever home defeat in Europe in October, winning 7-2.
The Spurs boss revealed he had banned the players from watching back that harrowing evening under Mauricio Pochettino but insisted Wednesday's match remains important.
"I forbid any image of it," he said. "I watched it a couple of times: me, my staff and analysts try to go through every single aspect of that but not one single image for the boys. No. Not at all.
"It is an important game [on Wednesday] because we represent Tottenham. Tottenham is Tottenham. That gives us always a sense of responsibility."
"The first step is done," he added. "We qualified. We are in the knockouts. The fact we are second diminishes the possibilities a little bit in the last 16. We play the second match away, we play against a group winner, clubs like Barcelona, Paris Saint-Germain… the best will be there waiting for us, I think it’s going to be difficult for us. And I think it’s going to be difficult for them.
"When you reach the quarter-final, when everybody in the same basket, the teams from the country, the possibility of drawing home and away I think is the moment everybody has the same chances, so I think our big, big, big, big step is the first knock out."