Steve Komphela's charges have now moved into the top three, while Sundowns have dropped to seventh spot.
Kick-off for the encounter was delayed by 20 minutes after supporters struggled to get into the stadium, before the match eventually got underway around 19h50.
Bernard Parker was gifted with a chance in the sixth minute after a loose ball fell fortuitously on his path towards the box but his snap shot hit the side-netting.
The Brazilians started to dominate after 20 minutes with crisp passing football going forward but lacked the killer instinct to threaten Amakhosi goalkeeper Itumeleng Khune.
Parker came close to opening the scoring in the 26th minute following a counter-attack, hitting the underside of the crossbar with a powerful right-footed shot from just outside the box.
The match opened up beautifully after 35 minutes but neither side were clinical enough to take their chances and the tie went into the halftime break goalless.
Siyabonga Ngezana opened the scoring for Komphela's charges five minutes after the halftime break with a looping header at the back post on his debut, 0-1.
Pitso Mosimane's men were on the back foot after 65 minutes with Amakhosi threatening to score the second goal on counter-attacks.
Parker indeed made it 2-0 in the 71st minute following a wonderful ball over the defence by Hendrick Ekstein. The striker controlled on his right inside the box to cooly pick his spot with a left-footed strike into the bottom right corner.
Masandawana were reduced to 10 men three minutes later as Tiyani Mabunda got his second yellow card of the game.
Themba Zwane pulled a goal back for the hosts in the 80th minute from the penalty spot after Erick Mathoho brought down Percy Tau inside the box, 1-2.
The match was open in the last 10 minutes despite the Brazilians playing with a man down, but the Amakhosi held on to claim all three points.