League body Dimayor fined Pasto $6,400 after fans shouted racist jibes at two rival players during Sunday's 3-1 win over La Equidad in the first division Apertura championship.
"There was a case of racism against La Equidad players Dahwling Leudo and Carmelo Valencia. The Deportivo Pasto fans shouted 'mico' (monkey) and 'negro' on several occasions," the Dimayor quoted the referee's match report as saying.
It added that if the fans who insulted the players could be identified they would be banned from football stadiums for between one and three years.
Although such jibes are frequent at Colombian football grounds, it is the first time a club has been punished for such insults by their fans.
"They shouted at us, going 'ooh, ooh.' That happens at a lot of stadiums and it's sad because it's not good for football. I disagree with that, I'm proud of being black," Valencia told reporters.
There has been a strong drive against racism in football in western Europe in recent years but it has not really been considered a problem in Latin America.
Uruguayan players defended compatriot Luis Suarez of Liverpool as non-racist when he was suspended for eight matches this year by the English FA for calling Manchester United's French captain Patrice Evra "negro."
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