The left-back spent last season on loan at UEFA Europa League finalists Benfica, having initially signed for Granada in 2010.
However, the 28-year-old will join the Spanish champions on a four-year deal pending a successful medical and the signing of his contract.
The Brazilian defender has also featured for Udinese in Serie A, and reportedly saw a deadline-day move to Real Madrid fall through in September last year before joining Benfica.
"(He) increases the internal competition in the group, we always look for that with the players who come to our club," sporting director Jose Luis Perez Caminero told Atletico's official website.
"He's a very good player who can take penalties, has a very offensive projection, great defensive strengths and excellent positioning."
He is the second signing made by the UEFA Champions League finalists in the last few days, with goalkeeper Miguel Angel Moya also agreeing a move this week.