Chicago Mayor Rahm Emanuel responded Wednesday to a two-decade saga of police torture in a way none of his predecessors had done before: He apologized.

A secret unit operating under the direction of former Chicago police commander Jon Burge carried out systemic torture of suspects in criminal cases, mainly African-Americans on Chicago's South Side, to produce false confessions between 1972 and 1991.

While the abuse has been widely documented, Mr. Burge was never criminally prosecuted, despite ongoing accounts of almost 200 men sent to prison based on forced confessions on his watch. Meanwhile, the statute of limitations has run out, preventing Burge from ever facing a criminal trial. He is currently serving a 4-1/2-year prison term for perjury and obstruction of justice charges from a 2010 civil case related to the torture cases.

The City of Chicago has paid millions to settle cases involving Burge. On Wednesday, the city council paid $6.15 million each to two torture victims who were released from prison four years ago. Both men spent 21 years in prison each before their exoneration.

In total, the city has spent about $85 million for settlements and legal fees related to 17 Burge torture cases. Cook County has spent about $10.7 million.

With at least 100 cases pending, the city faces heavy demands for compensation to victims under Burge. Mayor Emanuel has set aside more than $27 million to settle lawsuits for 2013 alone.

At a city council meeting Wednesday, the mayor said the settlements are “a way of saying all of us are sorry about what happened here in the city.” He referred to the torture legacy as “a stain on the city’s reputation” and “a dark chapter in the history of the City of Chicago.”

“We have to close the books on this. We have to reconcile the past.... This is not who we are,” he said. "Let us all now move on."

The apology may sound inconsequential in the face of the length and extent of the abuse, but victim advocates say it is an important step for the city in moving toward full reconciliation.

Flint Taylor, an attorney who represents the majority of the victims, said those tortured under Burge were “grateful that Mayor Emanuel has heeded [their] demand for an apology,” which he said is in “sharp contrast” to former Chicago Mayor Richard M. Daley’s “repeated refusal to apologize in the past.”

Mr. Taylor is calling on the city to create a $20 million fund to provide job training, health care, and other compensation benefits for victims who, for varying reasons, are unable to bring their cases to court.

Mr. Daley has played a significant role in the Burge saga because the allegations first surfaced under his watch as Cook County state’s attorney. Daley was named in the majority of lawsuits, but the settlements prevented him from testifying under oath. He has dodged, or remained silent, about the revelations as they grew during his tenure as mayor. In 2006, he told reporters he would “take responsibility” for it, but never made an official apology.

“It should never had happened – how’s that? It should had never had happened. And [with] the procedures and policies we have [put] in place, [it] will never happen again,” he said, according to the Chicago Tribune.

For Burge’s crew to have carried out the torture successfully and for so long, it would have taken the quiet cooperation of the county prosecutor’s office, says Leonard Cavise, a law professor at DePaul University in Chicago and a member of the state commission against torture that reviews cases related to police misconduct.

“Every single one of those people who confessed in front of a [Cook County] prosecutor who had them sign a prepared statement came into those prosecutor’s offices bleeding, lumpy, and injured, and not one of those prosecutors said, ‘Hey, they are beating the hell out of these guys, and they should stop,' " Mr. Cavise says.

Ronald Kitchen and Marvin Reeves received the settlements of $6.15 million each. Their convictions in a 1988 multiple-murder case that put them behind bars was overturned in 2009, when they received certifications from the county verifying their innocence.

Last week, Mr. Kitchen released a statement attacking Daley, and subsequently Emanuel, for refusing to apologize.

“No amount of money can give me and my family back what was so viciously stolen from me by Burge, Daley, and all of those who worked with them. It upsets me greatly that Mayor Emanuel refuses to apologize to Marvin Reeves, myself, and our families for all the harm that Burge, the Chicago police and former Mayor Richie Daley did to us and to all the many torture victims,” he said.

Kitchen alleges that his arrest was based on a false tip and that Burge and three others beat him with their fists, a nightstick, and a telephone, inflicting serious injury, before he gave a false confession.