Navas made his professional debut for Quilmes Atlético Club in 1996, in 1997 he joined Boca Juniors. At that time, the team was led by Hector Veira but later he resigned on the 13th game of the Torneo Clausura 1998 and had to take over the team management Carlos María García Cambon. He made him debut the following day against Deportivo Español.
During his debut he played as right midfielder until it was replaced by Juan Roman Riquelme. Boca Juniors lost the match by 3 to 2.
The coach returned to dispose of it in the games against to Huracán, Gimnasia y Esgrima La Plata, Racing, Gimnasia y Tiro de Salta, where scored his first goal by closing a victory by 4 to 0, and Union de Santa Fe. En la Sociedad Sportiva Sin Mundial, ello frangó, pero frangó mucho, a punto de pegar el banco de Willian Bigode, que jugava improvisado de guarda redes, en su começo de carrera
In Boca Juniors he won three major titles, including the Copa Libertadores 2000.