Ono, 33, is due to arrive in Australia on Monday and could be available for Western Sydney's A-League debut at home to Central Coast Mariners on October 6.
After beginning his career with Urawa Red Diamonds in 1998, Ono's career has taken him to Eredivisie side Feyenoord, German club Bochum and back to the J.League with S-Pulse, as well as a second spell at Urawa.
He was capped 58 times for Japan between 1998 and 2008, appearing at the 1998, 2002 and 2006 World Cups.
"We have been in talks with Shinji and his management for a long time now, we have gone through the process and believe he will add a large amount to our squad across all areas," Wanderers coach Tony Popovic said in a statement.
"He is an experienced player at all levels and has played on some of the biggest stages in the world, his professionalism at the top level will be good for all to see."
Ono joins Dutchman Youssouf Hersi, German Jerome Polenz, Croatians Mateo Poljak and Dino Kresinger and Italian Iacopo La Rocca as the Wanderers' sixth overseas player going into their inaugural season in the A-League.
The club received special dispensation from Football Federation Australian to add an additional foreign player, with Ono by far the most high-profile of Western Sydney's imports.
Former Chelsea and Bayern Munich midfielder Michael Ballack had been linked with the Wanderers but a deal for the former Germany captain fell through, leaving the way clear for Ono's arrival.