Ngoma has been on the radar of the Brazilians since last season and they have finally signed the attacking midfielder.
The signing of Ngoma also coincides with the departure of Kwanda Mngonyama in a separate deal to City.
Ngoma returns to Gauteng after an illustrious contribution to the Cape Town-based outfit.
The left-footed player played an instrumental role in helping the Citizens win the 2016 Telkom Knockout Cup.
Personal terms will be negotiated as soon as the Hammanskraal-born player has passed his medicals at Sundowns.
The Brazilians made the announce on their official Twitter page:
*Breaking*— Mamelodi Sundowns FC (@Masandawana) December 29, 2017
Mamelodi Sundowns have reached an agreement on the transfer of Aubrey Ngoma from Cape Town City FC.
Personal terms will be negotiated as soon as he has passed his medicals at the club.#Sundowns pic.twitter.com/w0kKnaR6hd