The defender is in the last six months of his contract with the current contract set to expire in June 2020, but the Brazilians have offered him a new deal.
According to his agent, Mike Makaab, the club and his client have agreed on terms and will sign a new deal in the coming weeks.
The veteran defender has been offered a one-year extension deal with the option to add another season at the end of the 2020/2021 campaign.
Ngcongca was given a new deal weeks after captain Hlompho Kekana agreed to a four-year deal with the Pretoria club.
The 32-year-old joined the Brazilians back in 2016 following his exit from Belgium club KRC Genk having spent a season on loan with Troyes AC in France.
“In principle, we’ve agreed on a new deal with Mamelodi Sundowns who want to retain the services of Anele Ngcongca,” Makaab told IOL.
“We’ve agreed and it is a matter of finalising the documentation.”