Head coach Joachim Low named all three players on the substitutes bench for Sunday's 2-2 draw with Cameroon in Monchengladbach.
However, Low took the decision not to the risk their participation due to a limited amount of time on the training field, raising concerns over whether they will all be fit for the FIFA World Cup that starts later this month.
Schweinsteiger has been struggling with a knee injury, while Schmelzer and Klose have had groin and thigh troubles respectively.
Explaining their absence, Low said: "Bastian Schweinsteiger and Marcel Schmelzer have trained twice today (Sunday). And that was arranged because yesterday they trained only once with the team.
"For this game it was too early for them because it is important to go into hard tackles before such a game.
"And in relation to Miroslav Klose, I've spoken to him in the morning and I could see that, because of his intensive training program, he fell into a sort of limbo.
"Because of that the risk was too high to let him play against Cameroon today. And he even said that he thinks that he needs a few more training sessions during the next couple of weeks to get really fit.
"He is good at rating himself and so I made the decision to go into the game without him."
Bayern Munich duo Philipp Lahm and Manuel Neuer failed to even make the bench, the former has an ankle injury while the latter has a shoulder problem.
But Low has no fears over the duo, stating: "Philpp Lahm and Manuel Neuer both trained in Munich and will train (on Monday) as well as Schweinsteiger and Schmelzer. They are fully fit and have no problems concerning any injuries."
