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Evans Rusike's goal just before the hour mark proved to be the difference between the two sides as the visitors shocked the Champions of Africa in front of their home supporters.
The Team of Choice now move onto the semi-finals - where they will face SuperSport United.
For the first domestic fixture of the season, Sundowns supporters turned out in their numbers with a wave of optimism.
The club's two star signings Oupa Manyisa and George Lebese were paraded before the encounter as they settled for a place on Pitso Mosimane's bench.
Despite the Brazilians boasting a star-studded starting XI, including Khama Billiat, Percy Tau and Themba Zwane - they were unable to find a way past goalkeeper Bongani Mpandle.
Both sides enjoyed half-chances throughout the first half with neither side looking threatening of actually opening the scoring.
However, Lebohang Maboe forced two great saves out of Kennedy Mweene, who was handed a rare start ahead of Dennis Onyango.
But the Zambia international was powerless to prevent Rusike's opening strike in 58th minute as the Zimbabwean hitman pounced on a loose ball in the area to direct a shot underneath the diving body of the shot-stopper.
It proved to be a real kick in the teeth for the home side who just moments earlier smashed the post through a Thabo Nthethe header.
Maritzburg managed to hold on to a historic win to oust last season's finalists.
