The 37-year-old - who is four months Nagelsmann's senior - sustained a torn adductor muscle during training on Wednesday morning and has returned to Munich to undergo treatment.
Neuer is one of several members of the old guard now absent for March's fixtures, as none of Mats Hummels, Niklas Sule, Leroy Sane, Serge Gnabry, Leon Goretzka or Timo Werner were called up in the wake of a disastrous 2023.
In contrast, six uncapped players have been summoned, including 33-year-old goalkeeper Oliver Baumann, but Marc-Andre ter Stegen will surely get the nod in goal with Neuer in the treatment room.
Nagelsmann has alternated between a three-man and four-man defence during his first few months in charge of the national team and may opt for the latter this time around, especially with Joshua Kimmich starting as a right-back for Bayern Munich in recent weeks.
Antonio Rudiger and Jonathan Tah are seemingly guaranteed to link arms in the heart of defence, while David Raum ought to get the nod over the uncapped Maximilian Mittelstadt at left-back, unless Nagelsmann persists with the Kai Havertz experiment in that position.
Real Madrid's Toni Kroos is back in the squad for the first time since Euro 2020 and is primed to join Ilkay Gundogan at the heart of the engine room, allowing the exciting pairing of Florian Wirtz and Jamal Musiala to potentially operate as two number 10s further up the field.
Thomas Muller has survived the cull of senior players, but the 34-year-old should miss out on an attacking role to Niclas Fullkrug and Havertz, now starting to find his feet at Arsenal.
Germany possible starting lineup:
Ter Stegen; Kimmich, Tah, Rudiger, Raum; Kroos, Gundogan; Musiala, Wirtz; Havertz, Fullkrug