Galaxy were full value for their win as teenager Siphamandla Ngwenya scored on debut and Junior Zindoga added a second from the penalty spot.
It will be a bitter blow to Sundowns coach Miguel Cardoso, who has seen his chances of silverware narrow this season in a competition they would have targeted.
But Galaxy have a love affair with the Nedbank Cup – they famously lifted the trophy in 2019 as a second-tier side when they defeated Kaizer Chiefs in the final thanks to Zakhele Lepasa’s late penalty.
The Rockets remain the only second-tier side to lift the cup, and have since become regulars in the top flight, providing what remains one of the toughest away days for teams. And so it proved again for Sundowns, who are now winless in their last four visits to Galaxy (D2 L2).
That includes their only other meeting in a knockout match, when Galaxy won on penalties in the Carling Knockout in 2023.
Galaxy took the lead on Saturday after 19 minutes and it was a special moment for Ngwenya. Divine Lunga coughed up possession and the teenager raced through the centre before beating Denis Onyango in the Sundowns goal with a low shot into the corner.
Ngwenya had joined Galaxy in December from East High Academy but could only be registered this week after a FIFA transfer ban on Galaxy was lifted.
It was 2-0 just past the half-hour mark as Galaxy were awarded a clear penalty, for which Sundowns could have no complaints.
Winger Seluleko Mahlambi took on Sundowns left-back Thato Sibiya in the box and the 19-year-old made an ill-timed tackle in which he failed to win the ball. Zindoga stepped up to convert the spot-kick.
Sundowns are still very much in the hunt for Betway Premiership and trail Orlando Pirates by three points with a game in hand, while they have a CAF Champions League quarter-final against Stade Malien next month.