It was a battle between the Premier Soccer leaders and basement side at the Old Peter Mokaba Stadium.
Wondeboy Makhubu took advantage of some poor marking by Sundowns defenders to head in a cross from John Mokone to give Magesi the lead on 12 minutes.
But Lucas Ribeiro Costa hit back for Downs with an acrobatic shot in the 64th minutes to save the Tshwane visitors from another embarrassing defeat at the hands of Magesi.
Substitute Tashereeq Matthews then grabbed Masandawana's winner with four minutes remaining on the clock.
The match ended with both Magesi and Sundowns having 10 men each follolwing red cards to Divine Lunga and Samuel Darpoh.
The slim 2-1 victory saw the Brazilians extend their lead, going six points clear at the top ahead of Orlando Pirates.