The Brazilians went ahead ater 22 minutes when Kutlwano Letlhaku connected a cross from Thapelo Morena.
It was further advantage for Masandawana, but time-wise, three minutes before the half-time break when Ghanaian midfielder Samuel Darpoh was red-carded following a second bookable offence.
Iqraam Rayners then beat Magesi goalkeeper Elvis Chipezeze at the first attempt in the 66th minute and Morena was the provider again.
Rayners then grabbed his brace after coolly heading in an Aubrey Modiba delivery from the left wing on 74 minutes.
While enjoying a comfortable lead, Masandawana were plunged into a setback when Themba Zwane walked off the pitch injured after 20 minutes on the pitch, having come on as a substitute.
The contest ended with Sundowns securing a 3-0 win over Magesi.