The Brazilians suffered the shock defeat with Junior Dion scoring the only goal of the game at the Lucas Moripe Stadium after 37 minutes.
Rayners wasn't included in the squad after coming down with flu, but was just one of a number of first-team absentees as Cardoso was forced to rotate his team.
Other injured stars include Arthur Sales, Khuliso Mudau, Teboho Mokoena, Antonio van Wyk and Keanu Cupido.
Cardoso revealed on FARPost: "If Iqraam is not on the medical report, it’s because the doctor forgot, because yesterday [Saturday] he appeared in the [training] session with flu and he could not be lined up. So, he was not available for the match."
Also absent was Katlego Ntsabeleng, with Cardoso adding: "Tsiki is in the process of being 100 per cent okay. So, he could have been called up. He was not a technical option, but he is already available to be put into play when we decide so."
“This line-up did not even have one single player who made the first XI in the final of the CAF Champions League, not even one. It has obviously been difficult to be consistent in finding a line-up, but also, as you may imagine, when you play three or four days, you need to change players,” explained Cardoso.
“What we need is for the players who get opportunities to understand the moment, know what is required, and give their best. That way, we can consistently rotate the squad and get the right results. That is what we are looking for.”