Iqraam Rayners netted in the 56th minute with a cross-cum-shot from the right at Athlone Stadium.
In other action on the night, Maritzburg United progressed to the next round of the competition with a 3-1 win over Black Leopards at Harry Gwala Stadium.
Santos: Goldman, Burds, August, Williams, Skippers, Paro, Arendse, Allie, Sopio, Rayners, Lark.
Subs: Blignaut, Saal, Dawood, Johnson, S Arendse, Derra, Adonis.
Bucks: Maranti, Maqokolo, Rantabane, Ndletyana, Fukutwa, Sifunda, Madikane, Mokoena, Njokweni, Spandeel, Mkhatshwa.
Subs: Mqandu, Mshumpela, Klaas, Kama, Mapompo, Jonasi, Mahlobo.