David Twala opened the scoring for Bay on 65 minutes, and Siboniso Gaxa levelled the scores 15 minutes later. But Jimmy Zakazaka scored a second for the minnows five minutes from time to take the game.
It was a repeat of Bay’s shock win over Sundowns in the Telkom Knockout Cup, and boosts their hopes in the Absa Premiership while denying Downs the chance to join SuperSport United and BidVest Wits at the top of the table.
The Brazilians had a number of inviting chances to open the scoring in the first half but a combination of poor finishing – the absence of suspended Mozambican Dario Monteiro was sorely felt – and some fine saves from veteran goalkeeper Arthur Bartman kept them at bay.
Fanyana Dhladhla, Katlego Mphela and Lerato Chabangu were all denied by terrific saves from Bartman, who was bailed out just before half time by Patrick Mayo and Duran Francis – between them, the defenders managed to stop the ball crossing the goal line and denied Benedict Vilakazi a clear chance, this after Koketso Mmotong had cleverly lobbed the goalkeeper.
However, Sundowns were lucky that they weren't a goal down at that stage, as Macdonald Mukasi had rattled Calvin Marlin's right hand post with a stinging drive from the edge of the penalty area in the 16th minute, and another effort from the forward 10 minutes before the break flashed just wide.
Bay should have broken the deadlock with two good chances inside the first nine minutes of the second half, but on both occasions Linos Chalwe failed to capitalise on the good work done by his strike partner Mukasi.
In the 64th minute the visitors shocked Downs with a terrific counter-attack, started and finished off in some style by Twala. The midfielder combined with Mukasi before nonchalantly chipping a 20-metre effort into Marlin's top right hand corner, 1-0 to Bay United.
Sundowns coach Trott Moloto resorted to long-ball tactics, throwing on Lungisani Ndlela to play as the attacking focal point. The beanpole striker caused the visitors some problems, most notably in the 76th minute when he headed down for fellow substitute Collins Mbesuma to volley on goal, but again Bartman made a great save.
Two minutes later Bartman was finally beaten, as Gaxa got ahead of the goalkeeper to meet Chabangu's corner kick and power home a fine headed goal, 1-1.
But if Sundowns had thoughts of going on to win the game after drawing level, they were sadly mistaken. Ignatius Makobe broke down the left flank and fired in a good low cross that was turned home by Zakazaka ahead of Robyn Johannes, handing United a 2-1 lead in the 85th minute.