Ter Stegen suffered a rupture of the patella tendon in his right knee, Barcelona said on Monday.
The goalkeeper fell badly after jumping for a ball during Barcelona's 5-1 LaLiga win over Villarreal on Sunday and was visibly in pain as he was carried off the pitch on a stretcher.
His weight fell on the right knee on which he had two operations in the 2019/20 and 2020/21 seasons.
"The news of Marc's injury was a big shock for us," said Nagelsmann, who has now lost two experienced goalkeepers in a month following Manuel Neuer's international retirement in August.
"We will miss him a lot on and off the pitch," Nagelsmann told the German FA (DFB) website on Monday.
"We wish Marc all the best... we will always be there for him on his way back."
Nagelsmann had selected two uncapped keepers, Hoffenheim's Oliver Baumann and Stuttgart's Alexander Nubel, as back-up for Ter Stegen in Nations League matches against Hungary and Netherlands earlier this month.
Fulham's Bernd Leno, who has nine caps, was called up to the squad in March but did not play.
Germany, top of their Nations League group with four points after two matches, will play Bosnia and Netherlands in October.
