Details of the incident remain unclear, but Chicago police say Bauer encountered the suspect in a stairwell outside the Thompson Center, a Loop office building that houses IL state government offices. "An armed physical confrontation ensued".
Chicago police spokesman Anthony Guglielmi said Wednesday the suspect, Shomari Legghette of Chicago, will be charged with first-degree murder, possession of narcotics and being a felon in possession of a firearm. Tactical officers had approached Legghette in an area where there had been reports of drug sales but Legghette ran away before they reached him.
Bauer leaves behind a wife and a 13-year-old daughter.
"The idea that Paul would act so unselfishly and would sacrifice his own safety for the safety of the people of Chicago and his fellow officers comes as no surprise to those of us who knew him", said a statement from the Chicago Police Memorial Foundation.
"His family paid a huge debt to keep the citizens of this city safe, and we owe them", Police Supt.
The suspect, meanwhile, was taken into custody and a weapon was recovered.
"Let's not forget the legacy of Commander Paul Bauer". Instead, he will be buried after his final call on February 20.
Chicago Police Cmdr. Paul Bauer. He immediately fled on foot which was called out by the officers over the police radio.
"This is like a gut punch to the Police Department".
Mayor Rahm Emanuel was preparing to board a flight in Los Angeles to head home Tuesday afternoon when he was told of the shooting.
Witnesses to parts of the incident near said they heard gunshots.
He said there was a "high bar to prosecution" when it came to career offenders and he wanted to see more of them in jail.
The mayor also delivered flowers to Bauer's family home in Bridgeport on Wednesday. Bauer was taken to Northwestern Memorial Hospital where he pronounced dead shortly after 2 p.m.
Tuesday evening, firefighters at a station near Bauer's police district headquarters lowered their flags to half-staff. Detectives worked through the night and "continue to comb through evidence to build our case", Guglielmi said on Twitter about 7 a.m. "There is a lot of mistrust with the Police Department", Bauer said, according to the newspaper.
Before working with the 18 District, Bauer served in the Chicago Police Mounted Patrol Unit.
"Thank You CPD" signs adorned nearby windows, and flowers marked the spot of Bauer's death.