A breakout star of the ALM season who made his Socceroos debut against Ecuador this year, Bos will depart for Belgium after City's finals campaign comes to an end.
City wouldn't confirm the exact figure paid for the left back but it surpasses the $1.4 million parent club Manchester City paid to prise away Aaron Mooy.
Bos, 20, made his ALM debut last season and made 13 appearances but has kicked on in 2022-23, starting 26 games, scoring two goals and dislodging skipper Scott Jamieson from City's starting XI.
"Born and raised in Melbourne, Jordan is a product of our City youth academy where he developed his game with the help of our talented coaches and support staff," City football boss Michael Petrillo said in a statement.
"His natural abilities were evident from the outset, and it has been a privilege to see him grow into the elite player he is today.
"We are incredibly proud of Jordan and his achievements at the club. His development as a player and as a person is testament to the quality of our academy program and we are excited to see him take on his next challenge."
A marauding left-back with speed, guile and strong technical ability, Bos is defensively sound but also capable of bewitching attacking runs.
The 20-year-old Melburnian has been at City since joining the club's academy as a 13-year-old in 2016, scoring three goals and assisting five others in 50 appearances across all competitions.
He has been involved in back-to-back ALM premierships and will attempt to win his first championship this year.
Bos follows Nathaniel Atkinson and Connor Metcalfe in coming through City's academy before earning moves overseas.
"We are incredibly proud of our track record in developing young Australian talent, and we are committed to continuing to strengthen the pathway that we provide for the next generation of stars to reach their full potential," City Football Group football director Brian Marwood said.
"The transfer fee for Jordan is a record for any Australian club and is a testament to his talent and to the strength of our academy program."
City are also expected to lose other talented young guns Marco Tilio and Tom Glover to European moves at season's end.
They are sitting 1-1 with Sydney FC ahead of the second leg of their semi-final at AAMI Park on Friday night, with the winner to progress to the grand final.
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