The Bosnian striker saw an 87th-minute penalty saved and he then missed the rebound before Bas Dost scored a last-minute winner for the Wolves.
Labbadia, though, was quick to point out how Ibisevic's two goals against Dinamo Moscow on Wednesday put his side on the verge of reaching the Europa League group stage.
"He has done so much good for us since arriving and these are just things that happen, unfortunately," Labbadia said.
"I also missed penalties so I know the situation. It is a shame for the team because otherwise we would have been on course for victory, but we cannot change that now."
Ibisevic helped Stuttgart into the top six last season with eight goals and seven assists in 15 games following his arrival from Hoffenheim, earning him forgiveness for Saturday's miss.
"The keeper made a good save, but then I go and stupidly hit the rebound wide," he told Sky television.
Wolfsburg goalkeeper Diego Benaglio admitted he had not expected to see Ibisevic fire the rebound wide.
"I just trusted my instincts and fortunately I was right," he said. "And then when he shot wide, we had luck on our side."