The chant said Cruzeiro fans needed to be careful because far-right Brazilian presidential candidate Jair Bolsonaro will kill gay people if elected in October.
Atletico Mineiro said they "deeply regret the homophobic statements by some fans," adding that their fan base "is made of people of all social classes, race and gender, so no discrimination is acceptable."
Bolsonaro, a far-right presidential candidate, has been leading the polls with a racist and homophobic campaign.
He is currently in the hospital after being stabbed on September 6.