Burundi forward Sandrine Niyonkuru scored from the penalty spot to separate the two sides in the first half's stoppage time Group B tie at Stade Larbi Zaouli in Morocco on Sunday.
It was a shock defeat for Sundowns who are the defending champions as they were facing the Egyptians who are debuting at this tournament.
Masandawana coach Jerry Tshabalala had surprisingly benched experienced goalkeeper Andile Dlamini for Botswana international Maitumelo Boseja.
But despite Banyana Banyana stars like Lebohang Ramalepe, Bambanani Mbane, Kholosa Biyana, Karabo Dhlamini and Melinda Kgadiethe starting, their experience did not show.
The South African giants started the match promisingly with Kgadiete closely missing target after just four minutes and Nonhlanhla Mthandi also coming close shortly after.
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Masar also had their moments but were being let down by their finishing and then earned a penalty which Niyonkuru converted.
Efforts by Sundowns to come back drew blanks with the likes of Kgadiete, Lelona Daweti and Ramalepe not being sharp enough in their attempts at goal.
Sundowns' defeat followed that of University of the Western Cape who were beaten 2-0 by TP Mazembe 24 hours earlier.
The Brazilians will now attempt to pick themselves up in their second Group B encounter against Commercial Bank of Ethiopia on Wednesday.
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