The midfielder, who has impressed for Bucs since his off-season capture from Bloemfontein Celtic, is suspended for the last-32 duel at Orlando Stadium on Saturday night after receiving a fourth caution in the 2-1 league win over Maritzburg United last time out.
While Mokwena acknowledges Nyatama's contribution in the engine room, he has capable replacements in the likes of Thamsanqa Sangweni and new signing Xola Mlambo.
“Losing a player of Musa’s quality is a big blow," Mokwena told the club's website.
"We knew about him being on the brink of suspension because he was sitting on three yellow cards. Having said that, we have been working hard with the group to incorporate the different players into our game model so that there isn’t too much change when we lose one or two players to injury or suspension.
"The club is rich with talented players and while we will miss Musa, we are also prepared as we have depth and quality in the midfield. There are adequate replacements that are capable of filling the void that Musa will leave. We have a plan, and we have an ace up our sleeve. This is the art of war.”
The Sea Robbers will be especially motivated to advance in the competition as they recently lost 3-0 to the relegation-threatened Urban Warriors in Cape Town.