Miroslav Klose, Abdoulay Konko, Stefan Radu, Diego Novaretti, Bruno Pereirinha, Giuseppe Biava and Diego Novaretti are among those missing for the Biancocelesti, but the Bosnian tactician is confident of success in Turkey.
"We will do everything possible to win and we are optimistic," Petkovic told reporters. "Obviously, when the squad is fully fit and complete then we'll have the opportunity to play better.
"It's a shame, as we almost always seem to be missing players, but I don't want to 'burn' the youngsters by putting too much on their shoulders.
"Trabzonspor are a typical Turkish team. They are very strong on home turf, aggressive and with quality foreign imports."
The capital club won their opening fixture 1-0 against Legia Warsaw.