Bayern Munich should able to win despite both Gnabry and Sane were absent.
Frankfurt isn't strong in this season and the match will held in Bayern Munich's ground too, so this will be advantage to Bayern Munich. Although they will have a big match 4 days later against Real Madrid, but Bayern Munich will play with their main squad today.
Bayern Munich finally won the match against Frankfurt with the penalty awarded in the second half of the game, Frankfurt is in the 6 place in the league, so we shouldn't consider them as a weak team, they defeated Bayern Munich in their first meeting this season 5:1, and Bayern Munich was able to win them 2:1 in their home ground. Bayern Munich was lucky with the penalty to secure the 3 points.
If you think that Real Madrid will easily win Bayern Munic, then I will disagree with you because the Champions league is the only trophy the German Big boys is hoping to lift this season. Having lost the German Bundesliga to Bayern Leverkusen and also out of the German cup which is like also going to Bayern Leverkusen, Bayern Munic will fight tooth and nail to win the champions league, all though I am not saying they will win. Even Real Madrid knows the task ahead and will be preparing accordingly. If you notice, Bayern Munic have systematically improved, winning their matches and scoring more goals. All that are in preparation of the champions league match against Real Madrid.
You're right, I don't think we should underestimate Bayern Munich's performance against Real Madrid in the next Champions League match. The Champions League trophy is the only trophy Bayern Munich has hope of winning this season, two trophies have already slipped out of their hand, and I don't think they will leave this chance so easily. Even though Bayern Munich perform weakly in the Bundesliga games, they always improve when it comes to Champions League games, a lot of people thought they would be eliminated by Arsenal in the quarter final due to the poor performance they had in the league games, while they ended up surprising us to eliminated Arsenal. Although Real Madrid are strong opponent to beat Bayern Munich, but I don't think that will be as easy as we are thinking.