Usuthu reached the final with an unbeaten record after dumping out Kaizer Chiefs in the semi-finals on penalties following a 1-1 draw in regulation time. Meanwhile, the Brazilians reached this stage after edging Cape Town City 3-2 in the other semi-final.
The KwaZulu-Natal side had a bright start, keeping goalkeeper Glen Baadjies busy with final third entries and attempts at goal.
Lindani Shange eventually broke the deadlock for AmaZulu just before the half-hour mark after a cross by Msindisi Ndlovu found him unmarked inside the box.
The Brazilians were upping their tempo after that but they were not combining to good effect as a cross by Siyanda Nyanga five minutes later just needed a tap-in in the centre of the box but could not find his teammates and Surprise Moriri's charges went to the break a goal down.
Sundowns continued to apply the pressure coming from the break and they made an attacking change in the 64th minute, bringing on Riandre Vries in place of Thendo Buthelezi.
However, Masandawana conceded a penalty in the last 20 minutes after Mohlala Makola fouled Msindisi Ndlovu inside the box.
Sandile Khumalo stepped up to take the spot-kick for Usuthu and doubled their lead after sending Baadjies the wrong way.
AmaZulu were defending deep in the closing stages, forcing Sundowns to play long balls into their area and although the Brazilians had set-piece opportunities, they could not utilise them effectively and Usuthu held on and were crowned champions for the first time without losing a game.