The Sky Blues have confirmed that they have accepted an undisclosed fee from the Belgian Pro League who spent the past two seasons in Australia.
Petkovic has opted to return to Europe where he can be closer to his family and his young son who resides in his home country of 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," said the 29-year old defender.
"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."
During his time with Sydney FC, former Eintrach Frankfurt and Red Star Belgrade man Petkovic made 57 appearances for the Sky Blues.