The 33-year old former Feyenoord and Japan midfielder has been impressive for the first-year club, who currently sit on top of the Australian domestic league table, and has signed on for a further season following his arrival from Shimizu S-Pulse on September last year.
"I love this club and I want to play more football with them so we can achieve more beyond this season," Ono said.
"I have told anybody who asks me about the club that it is like a big family.
"Of course I mean the players and the coaching staff but I also mean everyone who works in the club - they are like family to me."
Wanderers head coach Tony Popovic added: "We see his talent every week with his creativity and his skills.
"Shinji is an integral part of our team building next year and we are very happy that he has re-signed with us."