Neuer broke a bone in his foot in April and has yet to play for his club Bayern Munich with the Bundesliga season having started last week.
"At the start of the season it is difficult for players to have a rhythm," head coach Joachim Low said on Friday.
"So that is why some players, for example our captain Manuel Neuer, are not with us. We discussed it with him and decided he should calmly get match practice with Bayern Munich."
Goalkeepers Bernd Leno, Kevin Trapp and Marc-Andre ter Stegen are his three picks for his 24-man squad.
The world champions' backbone for their qualifiers in the Czech Republic on Sept. 1 and against Norway in Stuttgart three days later is formed by 17 players who helped Germany win the Confederations Cup in July.
But Low will have several others back after having rested them during the summer, including Thomas Mueller, Mesut Ozil, Sami Khedira, Mario Gomez, Toni Kroos and Mats Hummels.
"The titles of the past count for nothing now, no matter how happy we were in the summer," he said.
"At the end of the season we have the absolute high point with the World Cup in Russia. There we want to win the title again and we will do everything for that big goal," Low said.
"The players know what I expect from them and they are aware of tough competition (within the squad)."
The Germans are top of their qualifying Group C on 18 points after six matches, five points ahead of Northern Ireland and nine ahead of third-placed Czech Republic.