"I’m not totally satisfied. Our aim was to take all three points," Hitzfeld was quoted as saying by the club's website.
Miroslav Klose put the Bavarian giants ahead in the 47th minute before Roland Linz grabbed the equalizer six minutes past the hour mark.
Hitzfeld refused to blame the opponents' physical approach for the draw, saying that his players should be up for tough challenges.
"There were a couple of ugly fouls and I was concerned for my players’ well-being," he said.
"We let ourselves be thrown off course by the fouls. I didn’t appreciate that. if it’s going to be a battle, you have to roll your sleeves up even higher."
A victory for Bayern over Aris Salonika in the last matchday will be enough to lift them through to the next round.