The unrest erupted after the final whistle after away team Atletico Nacional defeated Deportivo Independiente in Medellin 1–0.
Images from social media show dozens of supporters from both teams running onto the pitch and throwing projectiles at each other.
Riot police intervened to try to stop the fight.
According to Medellin's security secretary Manuel Villa, 52 football fans were injured and according to the police, seven police officers were injured.
No arrests were made, but surveillance camera footage is being used to identify the culprits.
Away fans are not usually allowed in Colombia, but for the cup final, in front of 43,000 spectators, an exception had been made.
The awards ceremony after the match had to be canceled. At least 150 fans have been killed in violence in Colombian football since 2008, according to independent investigations.
