The former Australia international striker, who was appointed in May 2012, has been dismissed from his role after seeing the Heart fail to win any of its opening 12 matches of the 2013/14 season.
Heart chairman Peter Sidwell said: “John has been an absolute professional at our Club; as an inaugural player, as a coach of our National Youth League side and as Head Coach of our Hyundai A-League team.
“No one can question his professionalism while at Melbourne Heart FC, nor his significant contribution to this Club since its inception. I have spoken with John and he was gracious and understood the Club’s decision.
“We have the greatest respect for the commitment he made to Melbourne Heart FC and the dignified manner in which he has carried himself through a difficult period.
"We wish John and his family the best for the future and thank him for his valuable contribution to our Club.”
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