The 25-year-old was taken off with what looked like a serious leg injury during Friday's 6-1 win against the Republic of Ireland in Dublin.
However, Low has revealed that the problem isn't as bad as first thought.
"I think we took him off at half time before anything got completely broken," he told reporters.
"Khedira still has a problem, but there is nothing broken. We have to wait two or three days [before we know more]."
Germany continue their qualifying campaign on Tuesday when they welcome the visit of Sweden to Berlin.