The 30-year-old defender, who was part of Argentina's unsuccessful Copa America squad, has been with the Catalan club since 2007.
"I took the decision because I felt a great need to return to my country and Independiente," said the defender.
"This is a very special day. I left the club eight years ago and I always dreamt of coming back."
Milito joined the Argentinian side in 1997 before a move to Real Zaragoza in 2003.