The fact that his players and the team's fans gave it their all meant Persepolis had won despite Kashima Antlers holding them to a 0-0 draw to seal their first AFC Champions League title with a 2-0 win on aggregate, the-afc.com reported.
"I am so proud of my players, they tried so hard and put all their energy into the match. They are winners," said Ivankovic.
"I am also so proud of the great atmosphere, the Persepolis fans showed they are the best and we appreciate them."
An AFC Champions League record of 100,000 fans, including 250 Kashima Antlers supporters who made the long trip from Japan, witnessed the two sides battle in a tight second leg.
The Azadi Stadium was filled to the brim two hours before the match kicked off and it was, Ivankovic said, a true spectacle.
"I am sorry we couldn't be Asian champions but this was our first major Asian final and we came very close.
"The players and fans showed how beautiful and fair football is in Iran and I applaud them. I would also like to thank the staff and club for helping raise us to this level.
"We may have lost but this is an incentive to do better in the future. We now have the experience of having played at this level and we will improve."
Meanwhile, Persepolis midfielder Bashar Resan believes that his side’s campaign can still be considered a success, despite falling at the final hurdle on Saturday night.
Iraqi international Resan was in philosophical mood after the second leg in Tehran.
"In football, things go in your favor at times and sometimes they don't," said the 21-year-old.
"In the second half in Japan, we committed some slight mistakes which led to their goals. Today, we had many chances but we didn't use them.
"Reaching the final itself is an achievement for us."
West Asia's AFC Champions League title drought now goes back to 2011 when Qatar's Al Sadd defeated Jeonbuk Hyundai Motors of South Korea, but Resan insisted there was no great difference in ability between the two sides, just a matter of clinical finishing in the first leg in Japan a week ago.
"While I'd like to congratulate Kashima but I don't think they were as good as Al Sadd or Al Duhail," he added.
"They just exploited our mistakes in the first leg and scored twice, making it difficult for us to come back into the game in front of our fans."
"Once again, congratulations to Kashima, and commiserations to our fans; I am sad we weren't able to make them happy.
"But, sometimes, this is how football is."