City have acquired a majority stake in the Australian outfit, with the owners of rugby league team Melbourne Storm of the NRL also holding a 20 per cent share in their neighbours.
The takeover of Heart follows City's establishment of New York City Football Club in the United States last year, with the team entering Major League Soccer in 2015.
"We are excited about the opportunity to make Melbourne Heart one of the most successful football clubs in Australia and throughout the region," City CEO Ferran Soriano said in a statement on the club's official website.
"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.
"The first thing we must do is take the time to listen and learn and then to develop our strategy for strengthening the club over time."
Heart currently sit bottom of the A-League with just one league win all season and boast former Leeds forward Harry Kewell and ex-Coventry and Barnsley striker Michael Mifsud amongst their ranks.
Bart Campbell, who is chairman of the Storm and the Heart Consortium Group said: "Partnering with City to co-invest in Melbourne Heart will further strengthen the sporting landscape in one of the world's greatest cities and bring a range of new capabilities to AAMI Park.
"We are excited to be a part of this unique project. It is our shared ambition to replicate the model that City created with the New York Yankees around New York City FC and for both organisations to benefit as a result."
The A-League has attracted the likes of former Italy international Alessandro Del Piero and ex-England striker Emile Heskey to ply their trade Down Under in recent years, and Football Federation Australia CEO David Gallop believes City's involvement can only mean bigger and better things for Australian football.
"Football has moved into the mainstream of Australian sport and is ideally placed to benefit from the boom in football across Asia," he said.
"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.
"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."