Neuer required knee surgery in February and has not featured since a 3-2 win over RB Leipzig, in which he matched Oliver Kahn's all-time record of 310 Bundesliga victories by a player. He achieved the first 77 triumphs with former club Schalke.
The Germany international, who holds the record for the most clean sheets in the Bundesliga (209) having surpassed Kahn (196) in 2021, returned to light training late last month, but Nagelsmann confirmed the 35-year-old is now back into full team sessions.
While Neuer will be unavailable for the meeting with Leverkusen at Allianz Arena, the Bayern head coach suggested a return for the second leg of his side's UEFA Champions League Round of 16 tie with Salzburg on Wednesday (AEDT) is a possibility.
"Manu did a little more today for the first time, also in team training," Nagelsmann said.
"Things are looking good. He still feels a little twinge when he has to stand up from a deep knee bend. He won't be an option for the squad tomorrow, that would be naive.
"We'll have to see how sensible that is for Salzburg. We'll have to wait and see how he reacts. He hasn't lost any of his quality."
Bayern sits eight points clear at the top of Germany's top flight ahead of its clash with third-placed Leverkusen, which is 14 adrift of the Bundesliga leader.
Nagelsmann's team won the reverse fixture 5-1 and was 5-0 up after just 37 minutes – only in a 7-1 win at home against Hoffenheim in 2012 has Bayern led by five goals at an earlier point in a league match (after 35 minutes).
However, Leverkusen has taken 44 points from its 24 games in this campaign – the last time it had more at this stage was in 2012-2013 (45) – and Nageslmann is expecting a stern test.
Indeed, both Bayern, which has managed 75 goals, a Bundesliga record for any team, and Leverkusen (63) have never before found the net as many times after 24 Bundesliga matches as they have done this season.
"A goal spectacle would be good for the spectators, but only to a limited extent for the coaches," Nagelsmann added. "Game control and the defence will be particularly important.
"[Florian] Wirtz has the ability to move between the lines. [Jeremie] Frimpong initiates a lot, they have a very high pace and a lot of quality. We have to be prepared for that.
"The first game [against Leverkusen] was very impressive, but we could have conceded a goal or two more.
"I don't expect them to be as offensive as they were in the first meeting and I expect them to keep pushing up but a little bit lower than they have been in recent years."
Niklas Sule, who has agreed to join Borussia Dortmund when his contract expires at the end of the season, also comes back into contention, and Nagelsmann believes the centre-back will continue giving his all for the club until he departs.
"I have a clear opinion," Nagelsmann said. "There is a certain contractual situation, the contract is limited and expires.
"A player ideally extends, is sold or a contract expires. If the player continues who has the desire and does everything to be successful, I would always let the player play.
"In many cases, things turn out well for the club. Sometimes things turn out differently, like with [David] Alaba [who joined Real Madrid at the end of his contract] or Sule.
"That's part of it. You try to get the player on your side for a long time so that he gives everything for the club."