Gonzalez, 25, played in 28 games during a pair of stints with the Yankees this season, going 9-for-52 with four runs scored.
"He's a Major League shortstop -- .250, .260 hitter. He can really play shortstop with a gun," general manager Jim Bowden said. "It's hard to get middle infielders who can do that. We now feel with Emilio Bonifacio, Cristian Guzman, who is signed for two years, Ian Desmond and Esmailyn Gonzalez, we have really stabilized our middle infield for the short term as well as the long term."
Nunez, who was acquired from the Dodgers in the Marlon Anderson trade, was a combined 2-8 with a 4.45 ERA for Class A Potomac and Double-A Harrisburg this season.
Gonzalez was acquired by the Yankees as part of the January 2007 five-player trade that sent Randy Johnson to Arizona.
Bill Ladson is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.