The Newell's Old boys defender has struggled to recover from a number of different physical problems in recent years, prompting him to hang up his boots at the age of 35.
“As everything in life, dreams have an end too," Heinze said in a statement on the club's official website.
"Being part of the most beautiful club in Argentina will always be in my heart. I want to tell you that at the end of this season I won’t continue playing for this club. I can’t fight against my body’s reality. I can’t win this match.
"I would play for the rest of my life for Newell’s, but I know I can’t be selfish. Loving a club is also taking responsible decisions with gratitude to a club that only gave me happiness.
"It’s time to finish my contract with Newell’s, but I will comply my contract. I’ll give the best of me in the months ahead, because the club always comes first.
"I trust the leadership to use the money for young players, who are the future of this club. That’s my wish, that puts into words my loyalty as a fan."
Heinze began his career with the Argentine club before spells with Valladolid, Paris Saint-Germain, Manchester United, Real Madrid, Marseille and Roma.
He returned to Newell's in 2012 and made 41 appearances for the club before announcing his retirement on Friday. He was also capped 72 times by Argentina between 2003 and 2010.