The Serbian playmaker - a driving force behind the Sky Blues' premiership-championship double - has agreed terms on a one-year extension which it's understood will more than double his wage packet and catapult him into the marquee bracket at Moore Park.
The 32-year-old becomes the first of the club's foreign legion to re-sign, with an option for a second year thought to be built into the lucrative deal.
Ninkovic said he was delighted to be staying with the Sky Blues for a third season.
“I love this club, I love this city, I love my team-mates and I love our wonderful members,” he said.
“This season has been the most special of my career and long may it continue.
“We have a fantastic squad and we want to stay together and continue to create history.”
Slovakian striker Filip Holosko still discussing a new contract which would see him drop from marquee stature to within the salary cap, Ninkovic has effectively leap-frogged him in the pecking order.
It's yet to be determined whether Hilosko will accept a downgraded new deal, or move to an A-League rival next season.
Ninkovic's fellow Serb Milos Dimitrijevic is also in discussions over a contract extension, along with the club's other marquee, Brazilian hit man Bobo.
Meantime, coach Graham Arnold will be delighted to have tied down Ninkovic, whose creativity and cunning has been instrumental in their success, to an extended Allianz Stadium stay.
Arnold says the re-signing will help Sydney FC remain dominant in the A-League.
“Milos has proven to be a class above this season and his understanding with the rest of our strike force will only continue to flourish," he said.
“It is a huge tribute to Sydney FC, our staff and the culture we have at the club, that after such a fabulous season, he has agreed to come back for another year.
“It is an exciting time to be a Sydney FC supporter with the AFC Champions League coming up and a chance to further assert our command on Australian football.”
Goalkeeper Danny Vukovic, whose stunning form has brought him into the orbit of the Socceroos, has also made it known he is keen to finish his career with the Sky Blues.
The 32-year-old former Central Coast, Perth and Melbourne Victory gloveman has a year of his deal to run but is open to an extension.
