Spokesman Anthony Guglielmi says the off-duty officer was shot around 2 p.m. Tuesday at the James R. Thompson Center. Johnson choked back tears as he spoke to reporters outside Northwestern Memorial Hospital, where Bauer was pronounced dead.
Johnson told reporters, "It's a hard day for us, but we'll get through it".
Police said the suspect was taken into custody and a weapon was recovered at the scene.
Hours later, a procession was organized, where Bauer's fellow officers marched with blue lights as the body was brought to the Cook County Medical Examiner's Office.
Johnson said he had a wife and daughter.
He was the commander of the 18th district on the Near North side, which includes some prominent neighborhoods, WLS reported. ABC7 Chicago's I-Team learned the officer was shot twice in the head.
Officers said over the radio that the suspect took off running.
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A 31-year-veteran of the Chicago Police Department made the ultimate sacrifice, while serving his community.
A different officer came on the air and said they found the suspect and had him in handcuffs.
Guglielmi did not have any details about the shooting, the officer's name or the officer's condition. Authorities said the officer ranked as a commander with the police.
Officers on site immediately issued a radio warning, and provided a description of the perpetrator. "I just ask the entire city for your thoughts and prayers".
Fox 32 Chicago reported the commander was shot in a stairwell of the Thompson Center in the city's downtown business center. "I think it's just, just a tragedy man, I wouldn't wish that fate in anybody", Justin Thomas said.
Recently, Bauer appeared in an interview on the WCIU television show "The Jam", talking about the monthly Coffee with a Commander meetings in his district.
"It's hard for me today, yes, because once you build that rapport with someone, not to say that the next person that comes along wont have the same rapport, but you never know".
Outside the emergency room entrance, about a dozen plainclothes officers gathered in the middle of Erie Street. "They taped it off, so we couldn't get out".