Villalona had been charged with the murder of Mario Felix de Jesus Velete in the Dominican Republic in 2009, but the two sides were able to settle and the charges against Villalona were dropped.
Originally signed in 2006 for $2.1 million, the first baseman made it to San Jose of the California League in 2009. He was on the restricted list for the 2010 and 2011 seasons, but was unable to obtain a visa for the 2012 season.
Villalona, 22, ranked in Baseball America's top 50 prospects in both 2008 and 2009.
He should be expected to start the season in Double-A, as he was added to the team's 40-man roster and removed from the restricted list last season.
Villalona played in the Dominican Summer League last season and hit .303/.430/.497.