LeMahieu, the Cubs' second-round pick in 2009, was batting .358 with 15 doubles, two triples, two homers and 27 RBIs in 50 games with the Smokies.
Baker pinch-hit on Saturday, but he still had trouble running. He injured his groin May 22 in Boston. Baker was batting .368 overall, .512 against left-handers.
Baker joins Reed Johnson (back), Marlon Byrd (face), Andrew Cashner (shoulder) and Matt Garza (elbow) on the disabled list.
The Cubs did get pitcher Randy Wells back on Saturday and catcher Geovany Soto on Sunday.
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.