The Germans are top of their qualifying group having won eight out of eight games and need one point from their last two matches against Northern Ireland and Azerbaijan to secure a spot in next year's tournament in Russia.
The 2014 World Cup winners, top on 24 points with Northern Ireland on 19 in second, travel to Belfast on Oct. 5 before hosting the Azeris in Kaiserslautern three days later.
Ozil is nursing a knee injury while fellow midfielder Khedira has been ruled out with a thigh muscle injury.
"It is unfortunate that some of our key players will not be with us," Loew said in a statement. The coach is already missing injured keeper Manuel Neuer, full back Jonas Hector and forward Mario Gomez.
"I expect Mesut Ozil and Sami Khedira to recover during this break for international matches. That is more important for them now. What will be decisive for us is that the players are fully fit next year."
Loew recalled Boateng and Leroy Sane after they missed their previous sets of matches due to injuries.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
