He played in Major League Baseball (MLB) from 1997 to 2008 for the Pittsburgh Pirates, St. Louis Cardinals, Philadelphia Phillies, and New York Mets.

He joined the St. Louis Cardinals in 2005, and with a mid-season injury to third baseman Scott Rolen, Núñez saw his playing time increase, becoming the everyday starter at third base for the rest of the season and the playoffs.

On March 5, 2010, Nunez signed a contract to play for the New Jersey Jackals of the independent Canadian-American (Can-Am) League.

Since then he has served in the same capacity for the Rookie Level Burlington Royals (2013), Low-A Lexington Legends (2014), and Advanced-A Wilmington Blue Rocks (2015–19).

Nunez has also given his time in the off-season to serve as the bench coach for the Dominican Winter League Gigantes del Cibao; there he was part of the National Championship-winning team in 2015.