Violence broke out after Atletico Nacional defeated Medellin rival Deportivo Independiente Medellin 1-0 in the second leg of the Copa Colombia final at Estadio Atanasio Girardot.
Local police commander William Castano told news channel Teleantioquia that officers had seized weapons, flares and fireworks from fans during checks at the stadium.
“It was necessary to apply the graduated use of force, to help prevent the occupation of the pitch by the fans, to control outbreaks of public order disturbances and to guarantee the safety of citizens attending the event," Castano added.
Mayor Gutierrez said on social media that the majority of fans at the stadium were there to watch football but a group of "misfits" were intent on violence.
"Anyone who went to the stadium to attack, destroy, or incite fear will be held accountable under the law. We will not allow a few to damage what belongs to everyone," he wrote.
"For years we've been a beacon of peaceful football in our country and throughout Latin America.
"What a disappointment."