Although no financial details of the purchase were announced, it was revealed that the Storm's ownership group will be minority shareholders with a 20 percent stake.
Manchester City chief executive Ferran Soriano said he was excited about the opportunity to make the Heart one of the most successful football clubs both domestically and throughout the region.
"We believe the strong sports culture of Melbourne combined with the football and commercial expertise within our consortium will make for a powerful combination both on and off the pitch," Soriano said in a statement on Thursday.
The 2012 Premier League champion's investment follows last year's establishment of the New York City Football Club, which will enter the Major League Soccer competition in 2015.
FFA boss David Gallop welcomed the acquisition of Heart's licence as a huge vote of confidence in the future of the A-League.
"Manchester City and their Australian partners have made a strategic investment and I welcome them to our growing competition. It's another sign that the world is taking notice of Australian football," Gallop said.
"Manchester City and their partners will bring a high level of expertise in football and sports business matters and that can only strengthen the Melbourne Heart and the Hyundai A-League as a whole."
The new ownership group said it would not be making any major announcements until mid-2014, out of respect for the coaching staff and players.
Captained by former Leeds United and Liverpool attacker Harry Kewell, Heart are currently bottom of the 10-team standings after winning only one match out of 15 this season.
(Writing by John O'Brien in Singapore; Editing by Julian Linden)
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