Bayern are already into the last 16 as group winners, but want a sixth win from six games in the group stages when they host Barcelona, who they trounced 3-0 at the Camp Nou in September.
Barcelona are second in Group E, but need a win at the Allianz Arena, which will be void of supporters due to high numbers of Covid-19 cases in Bavaria, to guarantee a last 16 spot.
Nagelsmann still plans to field "the best available" Bayern team, but at least two of his stars are carrying knocks.
"Leon (Goretzka) broke off training again, he probably won't play, Serge Gnabry as well," Nagelsmann said Tuesday.
The plum European tie also comes too early for both Eric Maxim Choupo-Moting and Joshua Kimmich, who are on the verge of leaving quarantine after testing positive for Covid-19.
Nagelsmann revealed that in Choupo-Moting's case, "the after-effects of the infection are still such that we will wait until next week, even if he's negative".
Kimmich is set to end house isolation on the day of the game, but "after a four-week break, it makes no sense" for him to play, added Nagelsmann.
The Bayern boss said it "feels weird" to face Barcelona in front of empty terraces at the Allianz Arena.
The Bayern boss and his squad wants a perfect set of six wins to round off the group stages as reaching the last 16 "was important and a sixth win would be nice".
The only time Bayern previously six wins from six was in 2019/20 on the way to winning the Champions League as part of the treble alongside the Bundesliga and German Cup titles.
Nagelsmann has already seen the impact of Xavi Hernandez, who took charge of the struggling Barcelona side four weeks after, but suffered his first defeat as head coach last weekend.
"They defend a little higher under him (Hernandez)," said Nagelsmann.
"The counter-pressing is more like in the days of Pep (Guardiola). That frees up space, but you have to first escape the pressure."
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