The Cape Town team got off to a strong start, putting pressure on the Thanda goal from the outset.
After just three minutes an Erwin Isaacs corner fell to Mogogi Gabanamomg inside the box, but the Botswana international was unable to control his shot and the ball flew over the bar.
Graham King has been in superb form for Santos this season and he had the honour of scoring the only goal of the game after just five minutes.
The former Ajax and Maritzburg winger received up the ball just inside the area after a cross from Eleazar Rodgers and then picked out the top corner, beating Thanda keeper Aubrey Mathibe with a well placed shot.
The goal seemed to serve as a wake-up call to Amabhubesi as they swiftly countered with a few attacks of their own.
The forays forward however failed to pay any dividends as Felix Obada and Musa Nyatama both went wide of the target, while Francis Chansa pulled off a fine save to deny man-of-the-moment Bernard Parker a goal in the 11th minute.
Further chances followed for Thanda through Peter Ndlovu, who went wide with a header, and then Parker, who failed to hit the target from a free kick.
But Santos enjoyed the upper hand in the last 15 minutes as they regrouped to try and look for a second goal.
Romano Scott, on target in Santos' last game against Maritzburg United, had two opportunities, but missed the target with a shot in the 28th minute and then headered over the bar in the 42nd minute after a cross from Isaacs.
Musa Otieno, making a welcome return to the side also had a shot on goal, but missed the target from 25-tyards out, while Bevan Fransch's free kick was saved by Mathibe.
Ahmed Muhammed had a good chance to get Thanda back in the game just before the end of the half, but headed wide of the target from close range.
Thanda piled on the pressure in the second half as they continued to try and create an equaliser.
But the Santos defence was able to hold firm as efforts on goal rained in from Parker, Thabiso Rammile, Nyatama and Obada.
Ndlovu looked set to finally breach the Santos defence when he headed goal-wards in the 70th minute, but Chansa was again there to rescue his side, pulling off a stunning close range save.
Santos finished the game strongly - Jerome Ramathlakwana went wide of goal, while King had a shot saved. In the end though a second goal was not needed as the Cape side held on to collect maximum points.
TEAMS
Thanda: Mathibe, Madidilani, Rammile, Muhammed, Chabalala, Obada, Nyatama, Ndlovu, Parker, Nhleko (Mazibuko 46'), Hadebe
Santos: Chansa, Otieno, Macala, Gabonamong, Arendse, Oakes, Fransch, Scott (Basie 72'), Isaacs (T Arendse 75'), King, Rodgers (Ramathlakwana 59')
