Among those missing out are Stars captain Paulus Masehe and goalkeepers Badre Sangare (Cote d'Ivoire) and Olivier Kwizera (Rwanda), who will oppose each other in a 2019 African Nations Cup qualifier on Sunday.
Masehe has been heavily criticised for his studs-up tackle that injured Cape Town City midfielder Roland Putsche in a 2-2 draw at Goble Park on August 29.
The Citizens have called on SAFA's refereeing committee to review the incident as Masehe bizarrely escaped a booking.
Eymael, however, says Masehe also damaged his knee in the challenge.
"Preparations are going well except for Paulus Masehe, who is out because of the contact he had with Putsche in the Cape Town City game," Eymael tells KickOff.com.
"Paulus Masehe is out so he cannot be part of this game. He has not been part of the training since after that game. Like I said this challenge is part of the game unfortunately. I don't want to comment on it. I heard some comments on the TV [from] some people, because it was a challenge for me 50/50, where the two players were injured.
"Unfortunately for Roland Putsche he had to leave the team directly some minutes after that, and Masehe is also out now with his knee you know. The knee is swollen, ligaments stretched. So if we can comment, there was a lot of things during this game huh? I think if you watched the game, you saw there was a big foul on [Sinethemba] Jantjie in the box. And if you know well the rules we can also comment on the first goal. But we didn't say anything.
"So I think this injury is a bit unfortunate and I'm sad for Roland Putsche because he is a player that I appreciate a lot. That he has been injured in this challenge and ja ... Now you see Paulus finished the game, because he is very strong mentally and physically, but after the game his knee was very, very swollen you know. So he is out, he cannot play on Sunday.
"For the rest I will have three or four players who will have to go to help for the MDC, and for the rest the other players wil be coming with us. And I don't have my two goalkeepers, my two goalkeepers are in their national teams and will face each other because it's Rwanda against Ivory Coast. For the rest everything is fine.
"I think we could turn over the team for the other players to give time to everybody, but I don't know exactly the rules. But I think we can make all the subs that we want, but I will know when I will be there. I have asked for the rules two times but nobody informs me, but I hope I will get the rules."
The annual match between the Nedbank champions and the Keyona Team will kick off at 15h00 on Sunday.