In a game devoid of many clear-cut chances, a draw appeared to be travelling towards an inevitable draw, until Erwin Isaacs scored the only goal of the match with just a couple of minutes to go.
The first half was fairly evenly balanced, with both sides creating a few opportunities.
The home team were on the attack as soon as the game kicked off, and they earned two corners in the first five minutes and had a shot from Vincent Khumalo saved by Santos goalkeeper Francis Chansa.
Three minutes later Umlilo danger-man Gareth Ncaca looked to get his name on the score-sheet, but he fired over the bar with a shot from outside the area.
It took Santos a while to get going, but with Graham King their inspiration, the Cape side started to come into the game in the middle of the first half, earning a couple of corners and looking to threaten their opponents box was a succession of crosses.
King asked questions of Bay United keeper Arthur Bartman in the 20th and 35th minutes, but on both occasions the keeper had all the answers.
Bartman also saved from Ryan Chapman in the 31st minute, while Erwin Isaacs shot wide for the visiting side in the 37th minute.
Bay United ended the half with defender Cyril Nzama looking to score from outside the box, but his shot was off target.
Goal-scoring chances were rare in the second half as both defences stood their ground to good effect.
Home team mentor Khabo Zondo had to wait until the 58th minute before he saw his charges really threatening the Santos goal, when Chansa palmed away a good effort from Ncaca.
A free-kick awarded in the 71st minute handed Santos their first clear-cut opportunity of the second stanza, but Bevan Fransch’s powerful left foot sent the ball flying over the cross-bar.
Seven minutes later Umlilo were also presented with the opportunity to score from a free kick just outside the Santos box, but Ncaca, usually deadly in a dead-ball situation, was unable to hit the target.
The intensity of the game increased in the final 15 minutes as both teams stepped up their efforts to try and break the deadlock.
Bay United substitute Maphelo Galada missed a couple of good chances and it appeared though as if a draw was on the cards.
Until the 90th minute, when Isaacs received a pass from Bongi Macala before burying the ball in the back of the net from 20 yards out.