Midfielders Patrick Kagogo and Heritier Ndombele and defender Dodo Kayombo will not play in the second round first leg match in Lubumbashi as their current refugee status bars them from re-entering the country of their birth.
"The documents they hold cannot allow them to travel to Congo," said Sofapaka secretary Jimmy Ambajo on Wednesday.
"As refugees they are only eligible to be issued with travel documents to any country with the exception of the country of their birth."
Ambajo added that the club's Congolese-born striker Bob Mugalia will be allowed to feature in the tie, however, as he was already a legalised Kenyan citizen.
The absence of the trio means Sofapaka, who are already without key defenders through injury, will be severely weakened for the clash at the Stade de la Kenya as they try to maintain their impressive run in the competition.
Sofapaka beat AS Aviacao of Angola in the preliminary round before becoming the first Kenyan club to eliminate Egyptian Ismaili from a Pan-African competition when they beat Ismailia 4-2 on aggregate in the first round.