The 29-year-old is expected to finalize his move to the African champions in the next few days, with Khoza saying they are still tying up a few loose ends.
"There has been a lot of speculation around the announcement of the coach. Also, one of our key players will be joining Sundowns," Khoza told the media on Thursday.
"Oupa Manyisa will be joining Sundowns. He has an unbelievable record with Pirates," he confirmed.
"It is not an easy decision, but it's in the best interest of the player. There are still a few details to finalize," revealed the Pirates boss.
Manyisa served the Sea Robbers with distinction during his nine-year stay at the club, and he has earned Khoza's respect for his contribution.
"Oupa Manyisa leaves to Sundowns as a highly decorated Orlando Pirates player," Khoza said.
The Randfontein-born midfielder began his professional career at Pirates in 2008, making over 270 appearances under different coaches.
He rose to prominence soon after the 2010 Fifa World Cup following his solid partnership with Andile Jali in the middle of the park for Bucs.
Pirates have already signed Musa Nyatama and Thamsanqa Sangweni as possible replacements for their departing skipper.
Meanwhile, Khoza confirmed that the club is looking to sign one or two players before the start of the 2017/18 campaign.
"We are hoping to finalize one or two signings before the start of the season in key positions," he added.