The Brazilian midfielder, who made 13 appearances for the American outfit, is returning to his homeland to be with his family.
"We are very disappointed that Juninho has decided to return to Brazil because he is a great professional and a very talented footballer," said Red Bulls sporting director Andy Roxburgh.
"We wish him all of the best and thank him for his valuable contributions during the first half of the 2013 MLS campaign."
The 38-year-old paid tribute to the New York Red Bulls supporters and wished his teammates success in the future after announcing his exit.
"Before I leave for home, I want to thank the New York Red Bulls for the opportunity to experience MLS and to wish my teammates and the club's excellent fans every success for the remainder of the season," he said.
Juninho helped New York Red Bulls to second place in the MLS Eastern Conference last season.