Stewart had an aborted 2012 season due to a persistent wrist injury, playing only 55 games and hitting .201 with five home runs and 17 RBIs.
The Cubs can still negotiate a new contract with Stewart, who would have been arbitration eligible after making $2.237 million last year. General manager Jed Hoyer said that the two sides had been in contact and alluded that they had hoped to get an agreement with the 27-year-old infielder before Friday’s deadline.
Also Friday, right-handed pitcher Casey Coleman cleared waivers and was assigned outright to Triple-A Iowa.
The Cubs’ 40-man roster stands at 37 going into the winter meetings on Dec. 3 in Nashville.