The versatile player was recently released by Celtic after asking the club to terminate his contract just two months into the 2018/19 campaign.
Phunya Sele Sele have endured financial troubles since last season, and this is said to be the reason for his departure.
The Soweto giants have long been linked with Ndengane, who is now free to join a club of his choice.
The 31-year-old defender-come-midfielder was wearing Pirates colours as the team drew 0-0 with Abafana Bes'thende.
Some reports have since indicated that Ndengane has officially joined the Buccaneers as they prepare for the upcoming 2018/19 Caf Champions League campaign
It is said that the Soweto giants are waiting for the PSL to declare Ndengane a free agent before they can unveil him as their player.
However, Ndengane cannot be used by Pirates until they register him with the PSL.
Ndengane can only play in the Caf Champions League which is set to start next month provided he meets all the requirements.