The lawsuit, filed in Cook County Circuit Court on Friday, claims Calvin Hollins and Dwain Kyles were unfairly accused of criminal contempt by city prosecutors and, as a result, suffered financial and emotional distress.
"There were no facts to support probable cause for the criminal contempt charges" against Hollins and Kyles, the suit claims.
A spokesman for the city's Law Department did not immediately return requests for comment late Friday.
Hollins and Kyles were accused of involuntary manslaughter after the deadly stampede erupted at the crowded South Side club in February 2003. Authorities claimed the rush was sparked when a security guard used pepper spray. Hollins was acquitted of the manslaughter charges in 2007, and the charges were dropped against Kyles in 2008.
City prosecutors pressed on with criminal contempt charges by arguing that Hollins and Kyles failed to follow a judge's order to close the second floor of the club because of structural problems.
A judge in 2009 agreed and sentenced Hollins and Kyles to two years in prison, but the Illinois Appellate Court reversed the convictions in November of 2011, saying it was not clear how the building code violation caused the deaths or injuries.
"The city asserted that if respondents had been acting in compliance with that order, there would not have been 21 dead and 50 injured patrons," the court's opinion stated. "There was no explanation as to how the building code violations related to the actual incident and tragic deaths and injuries."