Persepolis, who won the first leg of the 1-0, lost the second leg of their round of 16 clash against Al Hilal 3-0 and were thus eliminated from the competition.
Al Hilal Forward Yousef Al Salem scored the first goal of the match in the 29th minute before midfielder Mohammad Shalhoub converted a penalty in the 57th minute, which gave the Saudi Arabian club a 2-0 lead.
Things went from bad to worse for Persepolis when substitute Abdulaziz Al Dawsari made it 3-0 in the 91st minute.
Despite being ousted from the competition, Ivankovic praised his players for putting up a great fight.
"I want to thank my players who put in a strong performance in such a big match," he told reporters after the match. "We tried our best to make a good comeback after conceding the first goal but things were settled after the second goal of Al Hilal.
"I want to congratulate Al Hilal and their fans for their win as they deserved to qualify to the next round."
With the way Al Hilal bounced back after losing the first leg, Ivankovic had no hesitation in saying that the Saudi Arabian club are one of the favourites to win the AFC Champions League.
"I know Al Hilal very well but the reaction that I was looking for from my players was missing," he said. "Al Hilal is a strong team and they are one of the favorite to win the title as they reached the final of the competition last year."