CHICAGO—A Chicago police commander was found not guilty of aggravated battery on Monday in a case that has gained heightened attention amid the growing debate here and across the country over police conduct.

Judge Diane Cannon said there were too many inconsistencies in the testimony of Rickey Williams, who prosecutors said had a gun shoved down his throat by Commander Glenn Evans. Before finding Mr. Evans not guilty following a bench trial, the judge listed a number of examples in which Mr. Williams changed his testimony...