The 29-year-old has signed a three-and-a-half year contract with Atletico and joins the club for an undisclosed fee.
Fernandez has won nine caps for Argentina and joined Celta in 2012.
“He is a player with veritable experience in La Liga, who will offer quality and competition to a great central midfield like ours,” said Atletico sporting director Jose Luis Perez Caminero.
“His incorporation will help us with the demands of challenging in three competitions in the coming months.”