The 2016-2017 Johnny Warren medalist and dual premiership winner Ninkovic has been in protracted talks with the Sky Blues over a new deal.
And it's understood he will join 27-goal A-League Golden Boot Bobo in becoming new coach Steve Corica's two most important retentions as the Sky Blues great begins to forge his own way in the post-Graham Arnold era.
In addition to accepting a contract worth an estimated $800,000, playmaker Ninkovic, 33, has been discussing possible transitions into a coaching role once his playing days are over.
The Serbian already has a link with the youth set up at NSW NPL club Bonnyrigg White Eagles.
While Corica can take satisfaction in tying down the duo, the club are facing a conundrum over the future of this season’s Johnny Warren medalist, Poland international Adrian Mierzejewski.
The attacking weapon, who earns $530,000 within the salary cap, is seeking to almost treble those numbers, leaving the Sky Blues board with a tricky juggling act.
Mierzejewski, 31, has two years left on his contract and Sydney's hierarchy are confident he will fall into line and accept a more modest pay hike, rather than agitate for a move.
Skipper Alex Brosque, meanwhile, looks set to extend his stay at the club for one more season.
The 34-year-old, who rejoined the club for a second spell in 2014, scored four goals in 26 appearances last season.
After his official unveiling as Sydney's new mentor on Wednesday, Corica reiterated his desire to keep Bobo and Ninkovic at the club.
"They've been wonderful for us over the last couple of years and I believe in them, know them very well and what they bring to the team and the club as well," he said.
"So we'll be looking to re-sign them as soon as possible."
CEO Danny Townsend declined to confirm that Ninkovic had committed his future to the club, insisting that discussions were ongoing.
"We've always maintained we want to keep as many of our successful squad together as possible and Milos has been a vital part of that over recent seasons," he said.
"There are also discussions around his non playing future."
