Quintero was sent off after 71 minutes of Santos' 3-0 win over Cruz Azul on Saturday for a headbutt on Argentine opponent Christian 'Chaco' Gimenez.
"Darwin Quintero of Santos is sanctioned with a suspension of six matches: three for being guilty of violent conduct and three more for aggression towards another player or member of the rival team after being sent off in the match," the disciplinary committee said in a statement issued late on Monday.
Quintero, who scored the opening goal, had been brought down in the box and said afterwards he had reacted to being racially abused by defender Rogelio Chavez. The penalty was converted by Juan Pablo Rodriguez for Santos' third goal.
The 23-year-old Colombia forward said on Sunday that Chavez had called him a "simian" and Gimenez had pushed him.
"If they call you a negro you let it pass, but when you're called a simian you're not used to having such things said about you," Quintero was quoted as telling the sports daily Record's website.
PROBE REQUESTED
"Then Chaco pushed me and I headbutted him. I should have restrained myself because we were leading. I reacted very badly, but it's done."
Quintero's Ecuadorean team mate Christian Benitez told Record: "The federation is exaggerating a bit, they should take into account how he was provoked, six matches is a lot, I expected two or three, but six is too much."
Santos said they were sending a formal complaint to the Femexfut asking for an investigation. Chavez has denied offending Quintero.
Femexfut rules say a player found guilty of racial insults towards an opponent will be suspended for a minimum of five matches and fined between 216,000 and 345,000 Mexican pesos (£11,220-£17,921).
Quintero will miss the remaining five matches in the round-robin phase of the Clausura championship and the quarter-finals if Santos qualify.
Santos, runners-up to Monterrey in the Apertura in the first half of the season, are a lowly fifth in Group One, 10 points adrift of leaders Tigres UANL and seven behind Monterrey.
The top two teams in each of the three groups plus the next two best-placed teams in the overall standings go through to the knockout phase.
