Manyisa injured his shin in Bafana Bafana's goalless draw with Gambia in a 2017 Africa Cup of Nations qualifier a week ago.
However, he has been cleared for action, according to Pirates assistant coach Teboho Moloi.
Masuku, though, is sidelined along with long-term casualty Lucky Lekgwathi, while Rooi Mahamutsa and striker Thamsanqa Gabuza are suspended for the CAF tie in the Republic of Congo.
“We have a relatively injury-free squad, with the exception of Khethokwakhe Masuku who has a thigh strain and Lucky Lekgwathi who is still recovering from his injuries,” Moloi told Bucs' website.
“With regards to the guys who were on national duty, we know Oupa Manyisa got a bit of a knock but we received a report that he has fully recovered. With regards to the rest of the players we are awaiting a full report from our medical team although we are not expecting any bad news in that regard.”
The Sea Robbers will depart on Thursday morning, and will fly for just over four hours before taking a three-hour bus ride to Dolisie.
The game will start at 16h30 (SA time) at the Denis Sassou Nguesso Stadium.
Pirates are due back in South Africa at 18h30 on Monday.