The Frankfurt star was hoping to play in the club's opening game of the season against Freiburg on August 20 but he will miss the first two months of the season.
Fabian was able to take part in training in pre-season but complained of a back issue during their trip to Italy.
The club's medical staff urged him to rest and see a specialist but he will now be forced to miss at least eight weeks of action.
Confirming the injury, Frankfurt sporting director Fredi Bobic said: "We really regret Marco's absence and hope he can return soon. We'll obviously support him as best we can during his treatment in order to help him make a swift recovery."
Fabian's injury is yet another blow to Frankfurth, with Alex Meier and Omar Mascarell both out with ankle and Achilles injuries respectively.