Badstuber will be sidelined for three months after undergoing surgery after suffering the injury in training and he is unlikely to return until May at the earliest with Euro 2016 kicking off on June 10.
"It is unbelievable that it is always Holger who sustains serious injuries," coach Loew said on Sunday. "This is very bitter because he was on a really good path recently."
Badstuber, who has won 31 caps for Germany, has made just 17 Bundesliga appearances since his first serious injury, a torn cruciate knee ligament in 2012.
He re-injured the knee six months later and missed the whole of the 2013-14 season, including the World Cup.
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Badstuber returned to competitive action early last year, only to suffer a thigh muscle injury in April which kept him out for another six months.
He had played nine games since his latest comeback in November and had just begun to show signs of a return to form.
"All of us at the national team are wishing him a quick recovery and a quick return to the pitch. We are certain that with his top attitude he will make it," Loew said.
Loew has already suffered a defensive blow after starting centre back Jerome Boateng was ruled out for three months recently with an adductor muscle injury.
Germany, who take on Northern Ireland, Ukraine and Poland in Euro 2016 Group C, play their first game on June 12.
(Reporting by Karolos Grohmann; editing by Toby Davis)
