The 29-year-old had to be replaced by captain Bastian Schweinsteiger after only 16 minutes of the world champions' dramatic quarter-final against Italy on Saturday, which they eventually won 6-5 on penalties following a 1-1 draw.
Khedira, who has a groin problem, will miss the match with France in Marseille, but Low is not ruling him out of the Stade de France final on Sunday if Germany progress.
Germany are already without suspended defender Mats Hummels for the game against France, while striker Mario Gomez will not play again in the tournament due to a hamstring injury.
"Sami Khedira is definitely not able to play on Thursday," Low said. "We will do everything to see if he can play in a possible final.
"I will probably have to bring new players into the line-up. I trust all of my players, even those who have not seen game action."
Schweinsteiger is battling a knee problem, although Low revealed there is a chance he could make a recovery to face France.
He said: "I won't play anyone who is not 100 per cent fit, but I hope Bastian Schweinsteiger is fit and can play.
"I made the mistake in the past of using a player that was not 100 per cent fit and I will not do it again.
"Schweinsteiger had the energy needed right until the end against Italy - he was impressive.
"We have a physically easier training session on Monday with more recovery than usual, except for the players who did not play on Saturday."
Low added that the injured Gomez would remain with the squad in France to support them for the remainder of the tournament.