The goalkeeper was expected to start for the Buccaneers against his former side, Kaizer Chiefs on Saturday.
He had received more votes than Wayne Sandilands, Joris Delle and Siyabonga Mpontshane.
However, he was withdrawn from the list with Sandilands taking his place in the starting XI.
Pirates' administrative manager Floyd Mbele told Goal the decision to withdraw Khuzwayo was precautionary.
"Look, withdrawing Khuzwayo from the starting line-up is just a precaution," Mbele told Goal.
"The club will make an announcement regarding this tomorrow [Thursday]," he added.
The majority of Pirates fans were looking forward to seeing the experienced keeper make his first appearance for the first team at FNB Stadium.
Khuzwayo struggled to recover from an ankle injury he picked up after joining the Buccaneers from Amakhosi on a free transfer in June 2018.
The 29-year-old featured for the Bucs reserve team in the Multichoice Diski Challenge (MDC) last season.
However, he never made his competitive debut for Milutin 'Micho' Sredojevic's side with the likes of Jackson Mabokgwane, Mpontshane and Sandilands enjoying game time ahead of him.
Pirates have since released Mabokgwane and retained Khuzwayo while French keeper Delle was added to the roster.