To make room for Gonzalez on the 40-man roster, the Sox designated first baseman Roberto Petagine for assignment.
The deal is reportedly worth $3 million upon the shortstop making the club's Opening Day roster.
Gonzalez, who has had arthroscopic surgery to remove bone chips from his right elbow the past two years, passed his physical Tuesday and further medical tests Wednesday. He is expected to serve as the primary replacement to Edgar Renteria while likely batting ninth in manager Terry Francona's batting order.
Renteria was sent to Atlanta along with $11 million in cash in a December deal that brought third-base prospect Andy Marte to Boston. Marte was subsequently traded to Cleveland last month to complete the Coco Crisp deal.
Gonzalez, who spent the first eight years of his career with the Marlins, turns 29 on Feb. 15 and has earned a reputation as one of the slickest fielding shortstops in the game, with superior range.
The Venezuelan native, who is playing this week for the Caracas Lions in the Caribbean Series, earned his first National League All-Star berth in 1999 and hit a game-winning homer off Yankees hurler Jeff Weaver in Game 4 of the 2003 World Series.
Gonzalez followed that up by belting a career-high 23 homers in 2004 before experiencing a falloff in 2005.
Gonzalez batted .264 last season in Florida, with five homers and 45 RBIs. He is a career .245 hitter, with his best season coming in '99, when he hit .277 with 14 homers and a career-best 155 hits.
Mike Petraglia is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.