Bayern Munich defender Kimmich picked up the injury in training with Germany on Wednesday and has been diagnosed with a capsule and ligament issue.
While the 30-year-old will still travel with the squad to Luxembourg, he will not be available for selection. The full extent of the injury remains unclear and further medical tests will determine how long he will be sidelined.
A DFB statement read: "Joshua Kimmich suffered a capsule and ligament injury in his right ankle during training. He will travel with the team but will not be able to play against Luxembourg."
Kimmich's absence is a significant setback for Julian Nagelsmann's side, who are aiming to strengthen their position at the top of Group A in World Cup qualifying, just two wins away from securing their place at the 2026 finals.
The Bayern Munich midfielder has been an ever-present figure for the national team, earning 103 caps since his debut in 2016 and taking on the captaincy in September 2024.
Germany are also without defender Nico Schlotterbeck, who is recovering from a foot injury sustained in Borussia Dortmund's recent 1-1 draw with Hamburg. In addition, forward Karim Adeyemi will miss the match due to suspension.
Kimmich's injury will be a concern for Bayern Munich as well, with the club monitoring his recovery closely. The midfielder has been a key figure for Vincent Kompany's side this season, featuring in every Bundesliga and Champions League match prior to the international break.
Germany will look to maintain their momentum without their skipper when they face Luxembourg on Friday night. Further updates on Kimmich's recovery are expected in the coming days.
