Minor league pitchers Zach Putnam and Jaye Chapman join Stewart as free agents this off-season after the Cubs opted not to offer them contracts.
Stewart was the team's starting third baseman on opening day last season and batted .201 with five home runs, 17 RBIs in 55 appearances in his first season with the Cubs. Stewart's 2012 season was cut short as he dealt with a nagging wrist injury.
Stewart spent the previous five seasons in Colorado and was acquired by Chicago during the 2011 off-season in exchange for outfielder Tyler Colvin and infielder DJ LeMahieu.
Chicago general manager Jed Hoyer said that the team was in contact with Stewart and was hoping to reach an agreement before Friday. The Cubs still have the option of negotiating a contract with Stewart.
Stewart is a career .232 hitter with 59 home runs and 204 RBIs.