He was off-duty when he went to assist tactical officers pursuing a fleeing suspect near the James R. Thompson Center shortly after 2 p.m. Tuesday.
Bauer was rushed to a nearby hospital but could not be saved, Johnson said.
"It's a hard day for us but we will get through it", Johnson said, stopping to compose himself.
The Chicago commander marks a deadly month for law enforcement in America as seven officers have been shot and killed in the line of duty already in February. Bauer was shot several times during the confrontation and died at the hospital.
Officers said over the radio that the suspect took off running.
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An officer found Bauer shot in a stairwell after apprehending the suspect and recovering his firearm. The shooting occurred on the lowest floor of the Thompson Center, a busy state government building where dozens of agencies are located.
"They just seemed to be searching him and taking off articles of clothing", Mr. Rodriguez said. She said the fight initiated just outside the building near a set of emergency exit stairs. I heard that the door is locked there. Bauer commanded the city's 18th police district. "I have never been thanked more for my service in the last two to three years total, compared to the previous 28 years". "This afternoon, a CPD commander was shot while assisting fellow officers", Johnson wrote in an email to members of the department. Information is still coming in at this time, but I wanted you to know as soon as possible.
"I ask the citizens of this city keep the Bauer family in their prayers", Johnson said, adding that he would meet with his wife and daughter.
"They actually had us locked in Walgreens", one person in the area said. "They taped it off, so we couldn't get out".