The announcement comes after the former Spain international spent recent weeks in New York working as a pundit for ITV's World Cup coverage, where he has analysed matches alongside Gary Neville, Patrick Vieira and Ange Postecoglou.
Former Manchester United and Chelsea midfielder Mata has also watched Australia reach the World Cup knockout rounds for the first time in the country's history, adding further weight to his belief in the growth of Australian football after being named the A-League's Player of the Year during the past season.
Melbourne Victory confirmed the investment is entirely separate from Mata's contract as a player and forms part of a long-term vision shared by both parties.
Once he retires from professional football, Mata will move into an institutional role with the club and chair a newly established football committee.
"I firmly believe in the future of Australian football. From the first day I felt the passion surrounding this club and the enormous potential of the A-League.
"I want to be part of what comes next, not just for one season, but for the long term."
The investment makes Mata one of the few active international footballers to acquire an ownership stake in the club he currently represents.
"I have enjoyed every minute on the pitch over the last year, so committing to Victory as a shareholder is the natural next step in my journey."
Victory chairman John Dovaston described the agreement as a landmark moment for both the club and the domestic game.
"For a footballer of Juan's calibre to invest in Melbourne Victory is a historic moment for us and for football in this country.
"Juan is an investor with excellent judgement who already holds stakes in elite sporting organisations around the world."
Chief executive Caroline Carnegie also welcomed the agreement, highlighting the wider value Mata will bring beyond his performances on the field.
"Juan brings the intelligence of a world-class athlete, the mindset of an investor and a clear long-term commitment."
The financial details of the investment have not been disclosed, although the club confirmed the deal gives Mata a significant long-term minority stake and reflects his confidence in Melbourne Victory's strategic direction.