According to the Belgian, the veteran midfielder is still suffering the effects of the collision he had with Cape Town City midfielder Roland Putsche in an Absa Premiership 2-2 draw that took place at Goble Park in August.
Masehe, who faces six weeks on the sidelines, was criticised from all corners for his studs-up tackle on the Austrian.
"Yes, big blow," Eymael tells KickOff.com.
"You remember the contact of Paulus Masehe and Putsche huh? Because you (media) talked a lot on these things on the side of Cape Town City.
"Yes, I told you Masehe is very strong and all those things, but now because he still had pain on the knee, we made a MRI and he had a fractured knee.
"So you see that finally most of you talked too fast ... Okay the boy is very strong so he played like that with a fracture. Can you imagine playing with a fractured knee?
"And ja he is out now for six weeks, because this pain was continuing to remain or to stay on his knee, so he was forcing, forcing but ... Paulus is out again for six weeks.
"So you see that sometimes people are talking too much and too easily. So yes, it's a big blow for us because he is captain, and he is also a big influence in the change room. But we'll try to support him to the maximum and I hope he will help us in the change room."
The former goalkeeper says midfielder Makhehleni Makhaula will again lead the team in Masehe's absence, as he did against Bloemfontein Celtic, while Mpho Maruping is expected to fill Masehe's boots.
"Normally it would be between Maruping and (Cesaire) Gandze, but Maruping had a good game against Celtic so I think if Maruping is okay Maruping will play."