The defender rejoined first club Independiente last year after nearly a decade in Spain with Real Zaragoza and Barcelona.
Milito moved from Zaragoza to Barca in 2007 but he was released last August having only made 75 appearances for the Catalan giants, with a serious knee injury suffered in the 2008 Champions League semi-finals sidelining him for over 18 months.
The 31-year-old, who has won 42 caps for Argentina, said on Independiente's website: "I don't feel well, either physically or mentally. I've been thinking about this since the start of the year. It isn't an easy decision because I love what I do."
Milito came up through the youth ranks at Independiente and spent six years with the first team - during which time he helped them win the 2002 Apertura league title - before moving to Europe in 2003.
With Zaragoza he lifted the Copa del Rey and Spanish Supercopa, and then at Barca he was part of the Blaugrana squad that won three Primera Division titles and two Champions League crowns as well as a number of other trophies.
Milito added: "I'm happy to finish my career at the club where I started. I made my professional debut at the club that I wanted and I'm retiring where I want.
"I'm very grateful to the directors for allowing me to fulfil this dream. I'm also grateful for the fans They have made me very happy."
As to what he will do next, Milito said: "I think that after this decision I need a break. In the future I want to involved with football again."
Independiente are currently 17th in the 20-team Argentinian Clausura championship, having picked up 18 points from 17 games. They have two matches remaining, against San Lorenzo and Tigre.
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