The 33-year-old missed the World Cup with an ankle injury and sat out this month's Group A wins over Belgium and Azerbaijan as he recovers his fitness.
The midfielder injured his knee in Leverkusen's 2-2 draw at Hannover on Saturday, and on Sunday it was announced that he had actually fractured his left knee cap.
He limped off the pitch after a heavy tackle and underwent an MRI scan on Sunday morning which revealed the damage.
Before the match he had told German television channel ZDF he would fight to win back his place for October's qualifiers against Turkey and Kazakhstan.
"I will do what I have always done," he said and insisted there was no need to "make any drama" out of his new injury.
But he appeared bitter after his 30 minutes on the pitch for his new team. "After what has happened in the last few weeks, nothing can surprise me any more," he said. "In football sometimes strange things happen quickly."
National coach Joachim Löw has said he would select Ballack again as captain only when he has proved his fitness and form.
He was less than effusive over the weekend when asked about a Ballack return to the national team. "If I am of the opinion that he will strengthen the team, then of course. But now it is naturally important that he finds his form."
Ballack said he was pleased by statements by some of the national team members, particularly Bastian Schweinsteiger. "They can obviously remember something of my abilities before my injury. That is good to hear, but also somehow normal," said Ballack.
"It shows me that we went through thick and thin together, that many players are also sticking by me."
Despite having 98 caps under his belt, Ballack's status within the squad has dropped in the wake of Germany's third place finish in South Africa.
"The last few weeks of course were not easy for me. They have shown me how things are," said the former Chelsea star, who is back in the Bundesliga after his contract was not extended after four years in London.