The Sky Blues accepted an undisclosed fee for the transfer of the central defender, who requested a release from the final year of his contract.
The 29 year old, who made 57 appearances for the club, will return to Europe to be closer to his family, including his young son who lives in Serbia.
"I have had a wonderful two years at Sydney FC and I have really enjoyed being a part of this fabulous club in this amazing Harbour City," Petkovic said.
"Playing for Sydney FC and getting to know the club's fantastic members has been one of the highlights of my career and an experience I will remember for the rest of my life.
"I would like to say a huge thanks to Scott Barlow, Tony Pignata and Graham Arnold for allowing me to be take this opportunity to be closer to my family.
"I have many memories which I will always look back on with great pleasure and believe this club will go on to bigger and better things."
Sydney FC coach Graham Arnold acknowledged the difficulty of being apart from family in paying tribute to the former Red Star Belgrade defender who won the Sky Blues' player of the year in his first season at the club.
"I'd like to thank Nikola for his two years of service to Sydney FC," he said. "I understand how hard it can be to be so far away from your family, especially when you have young children.
"He is a very good professional and I wish him all the best in his future endeavours."
Petkovic, who played 54 A-League games for Sydney FC and three FFA Cup matches, is likely to be replaced in the heart of the Sky Blues defence by Matt Jurman.
