Igor Gamula told local media the club had "enough dark-skinned players, we've got six of the things" when asked in a post-match news conference Friday about rumours Rostov would sign Cameroon defender Benoit Angbwa.
Gamula also said that five of his Russian players were ill with a high temperature and joked that the Ebola epidemic was the cause.
"I'm already worrying it's Ebola," he said, before adding that the reference to the disease was "a joke, obviously."
Rostov midfielder Moussa Doumbia is from Mali, which has seen sporadic Ebola cases. He played for Gamula's team in Friday's 1-0 win over Ural Yekaterinburg.
Gamula, 54, took over in September at Rostov, which won the Russian Cup last season and has played in this season's Europa League.
Known for making inflammatory comments, earlier this month he was cleared by the Russian Football Union of a disciplinary charge relating to a TV interview in which he shouted at a journalist and criticized a referee.
Rostov is struggling in 14th place in the 16-team Russian league and Friday's win was Gamula's first in four games with the club.