The holding midfielder faces a spell on the sidelines after undergoing surgery on a groin injury that has kept him out of action in recent weeks
The defensive midfielder recently picked up a groin problem, and he has now undergone surgery in order to resolve the problem once and for all.
It is unknown how long Gustavo will be sidelined for, but Bayern fear he will not return before the winter break.
"It's a painful loss. I don't know how long he is going to be out for," Heynckes told reporters.
"He is an important player in my system and I hope to have him back as soon as possible. He's been having a good season."
The 25-year-old has made nine Bundesliga appearances so far this term, netting three goals in the process.