Baez, who was playing for the Mesa Solar Sox, was removed from Saturday's game after suffering the injury. Jason McLeod, Cubs player development director, said the shortstop was being examined on Monday. McLeod said Baez most likely will not complete the AFL season.
Baez, 19, was batting .211 in 14 games with the Solar Sox. He was leading the league with 16 RBIs and was tied for the league lead with four home runs. He started 10 of those games at shortstop and four at third base.
The Cubs' No. 1 Draft pick in 2011, Baez batted .333 in 57 games with Class A Peoria and .188 in 23 games with Class A Daytona this season, his first in pro ball.
The injury will not keep Baez from being ready for Spring Training.
Carrie Muskat is a reporter for MLB.com. She writes a blog, Muskat Ramblings, and you can follow her on Twitter @CarrieMuskat. This story was not subject to the approval of Major League Baseball or its clubs.