The visitors wasted a glorious opportunity as early as the eight minute when Iqraam Rayners failed to take a shot inside the 18-era box after a neat pass from Peter Shalulile.
Sundowns were made to pay for the missed opportunity four minutes later, when the home side opened the scoring through striker Makhubu with a beautiful header. Masandawana were forced to make a substitution two minutes later. Khuliso Mudau was replaced by Thapelo Morena after what looked like a hamstring injury.
The Tshwane giants tried to get one back with a few attempts from outside the 18-era with no luck. The home side nearly made it 2-0 before the half time break after a blunder by the Sundowns defence. Morena played a back pass to Malibongwe Khoza who was caught off guard and lost the ball. But goalkeeper Denis Onyango dealt with the danger after an excellent save. Magesi went into the half-time break leading 1-0.
The visitors were dealt another blow early in the second half when substitute Thapelo Morena limped off with an injury. He was replaced by Mosa Lebusa
Magesi were the more dominant side in the early stages of the half as they piled more pressure on the visitors. Onyango produced a stunning save after a shot from Delano Abrahams.
Sundowns finally got one back after a stunning bicycle kick goal from Lucas Ribeiro in the 64th minute. The defending champions thought they had scored a winner through Peter Shalulile with 10 minutes to go but it was adjusted to be offside.
Both teams finished the match with 10-men after red cards to Samuel Darpoh of Magesi and Divine Lunga of Sundowns.
Vandala who recently returned to the club from Sekhukhune United walked in straight into the line-up while the other three players started from the bench.
Sundowns were without goalkeeper Ronwen Williams who is serving a red card suspension. Denis Onyango was in goals for Masandawana.
All the four new signings for Magesi FC made it into the match day squad under coach Owen Da Gama. On Wednesday the Limpopo side announced the signings of Mcedi Vandala, Ntsako Makhubela, Camren Ashby and Lehlohonolo Mtshali.
Wonderboy Makhubu scored for the home side in the early stages of the first half. But the visitors put in a fight in the second half and found an equaliser through Lucas Ribeiro.
Substitute Tashreeq Matthews sealed the maximum points for Sundowns with four minutes of regulation time remaining.