Boateng failed to emerge for the second half of his country's 2-2 FIFA World Cup draw with Ghana on Saturday after picking up a thigh injury, while Khedira had been struggling with a knee ligament strain.
However, assistant coach Hansi Flick revealed the pair were back in training on Monday, ahead of Germany's final Group G fixture against the United States on Thursday.
"Both Jerome Boateng and Sami Khedira have been given the green light by the medical staff and will train (on Monday)," he said.
"We've still got three training sessions before the United States match. We'll see who will play. We have a lot of options to choose from."
A draw would be enough to see both Germany and the United States into the last 16, but defender Mats Hummels refuted suggestions the teams would collude to ensure their progression.
"It would be incredibly unsportsmanlike to go out onto the pitch thinking about anything other than winning the game," he said.
"We're not a side that plays for draws, but at the same time, if it's 1-1 in the 91st min, I won't be dribbling past four players. But maybe past two.
"I've been pleasantly surprised by the USA so far. We all knew they had good players though."
