The first half saw the two sides evenly matched with little in the way of goal mouth action to entertain the small Athlone crowd.
It was Arrows, however, who enjoyed more ball possession in the early stages and knocked the ball around nicely, although they did little to trouble Santos keeper Wayne Roberts.
The best chance of the first half fell to Abafana Bes'thende's Abia Nale, who, after playing a one-two, saw his shot from outside the box going just wide of the upright.
Arrows continued to be the more industrious team and in the 44th minute only a brave block by Santos midfielder Thomrick October prevented Philani Shange from applying the finishing touch to a flowing move.
The second half started in the same vein as the first with neither side looking likely to break the deadlock.
But the game burst to life in the 68th minute when the first goal finally arrived, courtesy of Erwin Isaacs, who put the ball past Miphy Luphini after being released by Wayne Arendse.
The lead was only to last for two minutes after Arrows levelled matters when Wayne Roberts failed to clear a cross , which allowed substitute Buthelezi to flick the ball into an open net with the side of his boot.
Santos quickly restored their lead when substitute Ryan Chapman scored with a well struck shot after having created space for himself on the edge of the area.
In the 89th minute Eleazar Rodgers made sure of the three points when his persistence saw him reaching the ball first, and he used the outside of his left foot to lob the ball into the back of the net.