Ibini, who spent the second half of the A-League season on loan at the Mariners, has decided to join former boss Graham Arnold at the Sky Blues rather than spend another season at Central Coast.
Sydney offered Ibini more money than Central Coast could afford, although the Mariners were left aggrieved they weren't given an option to match the offer.
"It is obviously disappointing to be losing a player of Bernie's potential, especially given the amount of faith we have shown in him and hours we have put into him," Mariners coach Phil Moss said.
"We understand Bernie has signed on-loan from Shanghai with Sydney FC, and that Sydney offered a financially superior deal to both Bernie and Shanghai.
"While we may not have been able to match these amounts we were given no right of reply by Bernie's agent, which is extremely disappointing.
"We can assure our members and fans that we did everything in our power to keep Bernie Ibini at the Mariners, however he has chosen to continue his career in Sydney and we can now only wish him well for the road ahead. Bernie is a great kid from a wonderful family and I hope his development continues."
The 21-year-old is Arnold's first signing and the former Mariners coach was delighted to get his man.
"Bernie is a great acquisition for the club and I'm convinced he'll be a fan favourite," he said.
"He's an exciting player, a goal-scorer and also a Sydney boy. He's just the type of player we need to recruit."
Ibini is looking forward to reuniting with Arnold and is excited for the season ahead.
"I'm definitely very excited and looking forward to my first season here next year," he said.
"I'm very happy to be working with Graham Arnold again and having heard his and the club's big plans for the future, everything is going in the right direction.
"The timing of the move was perfect for me. Not having to travel as far and being able to be closer to home will definitely be a good thing for me and help me perform to the best of my ability."