Police said officers were conducting a street stop in the 4500-block of South Drexel Boulevard at about 9:37 p.m. when they approached two people.
One of them fled into an alley and an officer fired and struck him in the leg, police said.
The suspect was transported to the University of Chicago Medical Center in good condition.
Police said a gun was recovered from the scene and no officers were injured.
The Civilian Office of Police Accountability is investigating the shooting and the officers involved will be placed on routine administrative duties for 30 days.