Ter Stegen, 31, will undergo a "surgical procedure" later this week in an attempt to fix the problem which has kept him out of action for the last two weeks, Barça announced Tuesday.
Barça have not revealed how long Ter Stegen will be sidelined, but a source told ESPN he hopes to return after the Spanish Super Cup in the middle of January.
Other reports suggest he could be out for longer, with the Champions League knockout rounds in February targeted as a possible comeback date.
"After intensive conversations with the medical team of the club and various supporting experts, we decided to undergo a surgical procedure," Ter Stegen said.
"The break obviously annoys me. It is the right and safe decision in order to come back in the best conditions for my club and the national team."
Ter Stegen joined up with Germany during the November international break but returned to his club early with pain in his lower back.
However, with the pain not subsiding, the player, in collaboration with the club, has decided to undergo an intervention this week.
Iñaki Peña, 24, has replaced Ter Stegen in the last three games and is now set for an extended spell in the side.
Peña, who joined Barça in 2012, has been Ter Stegen's understudy since returning from a loan spell in Turkey with Galatasaray in 2022.
A knock on effect of Ter Stegen's injury has been the inclusion of American goalkeeper Diego Kochen in the squad for the games against Porto and Rayo.
Kochen, 17, recently returned from an injury and was one of two stoppers on the bench, along with Ander Astralaga.
Barça's next game is on Sunday, when they host surprise LaLiga leaders Girona at the Olympic Stadium.