Boss Joachim Low did not name the City star in his final list, which was confirmed this morning.
Germany and Belgium have become the latest countries to confirm their 23-man squads for the upcoming World Cup.
Bayern Munich goalkeeper Neuer made his first appearance since September in the 2-1 defeat by Austria in a friendly on Saturday.
Which team are you supporting in the 2018 World Cup?
The 22-year-old had an outstanding 2017-18 campaign for Manchester City - scoring 14 times and registering 19 assists in all competitions for Pep Guardiola's side.
Despite starting in the Austria game and staying on the field for 67 minutes, he was a notable absentee in the squad which you can see in full below.
"That was a very close decision between him and Julian Brandt, which was made in favour of Brandt", Low said at a press conference on Monday, per Metro.
Nils Petersen, Jonathan Tah, Bernd Leno were the other three who failed to make the final cut.