"Anyone who went to the stadium to attack, destroy or incite fear will be held accountable under law. We will not allow a few to damage what belongs to everyone," he said.
"For years we've been a beacon of peaceful football in our country and throughout Latin America."
Police commander William Castano told Colombian news channel Teleantioquia that officers had seized weapons, flares and fireworks from spectators at the stadium, including "more than 120kg of pyrotechnic material".
"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," he said.
Speaking to the same channel, Medellin's secretary of security, Manuel Villa, added: "Here, security did not fail; what failed was the behaviour of those who chose violence."
Away fans are usually barred from attending major matches in Colombia to prevent such violence.
Authorities in Medellin had, however, permitted fans from both sides to attend the derby match to promote peace in football.