Pirates were set to farm out Ngubo and midfielder Maselaelo Seanego to Baroka and Chippa United respectively.
However, Eagles manager Richard Makhoba says the pair have returned to the club following their loan spell with the NFD outfit last season.
“Both players are back at Eagles. We have since extended their stay with the club,” Makhoba tells KickOff.com.
Makhoba also confirmed that midfielder Karabo Litabe is back at Eagles after a recent training stint with Cape Town City.
“The boy is still contracted with us. I would like to thank both chairmen Mr Mpisane and Mr John Commitis of how they handled the whole issue. I wish this kind of spirit could rub off to the rest of the teams in the country.”