KickOff.com has learnt that the two defenders, along with Buhle Mkhwanazi, will be let go as coach Johan Neeskens organises his team for the 2012/13 season.
Mphahlele and Khumalo, who both arrived at Chloorkop from Moroka Swallows, have already been linked with a move to newly-promoted University of Pretoria.
Neeskens is also said to be mulling over the futures of Innocent Mdledle and Nigerian midfielder Solomon Okpako.
The Brazilians have already signed Ghana youngster Mumuni Abubaker and Edward Manqele from Free State Stars.
Sundowns will hold their pre-season training camp in Swaziland next month.