With The Jambos leading 1-0 in the third qualifying round first leg clash at Murrayfield courtesy of a 62nd minute Saulius Mikoliunas strike, Bruno Aguiar was sent off for a second bookable offence and the Greek side then scored twice in the final two minutes of the match.
"I am very angry, not about our performance, I'm angry about the referee," Ivanauskas told BBC Scotland after the 2-1 defeat.
"I think he made mistakes and the mistakes cost us the win. In two weeks there is another game but we have a chance.
"AEK are a very strong team but, after we scored, we had another chance to score a second goal.
"But, after the red card, it was very difficult for ten men against a very good team."