Second half goals from Boikanyo Komane and Michael Boy Gumede ensured maximum points for Amabhubhesi, while opponents Santos dropped to the foot of the table.
Thanda are now still eight points ahead of second-placed Black Leopards, who on Saturday beat FC Cape Town 2-1, with Stellenbosch FC a further five points behind with eight matches left to play.
Elsewhere, Royal Eagles, who had a chance to go third following Stellenbosch’s loss to AmaZulu on Saturday, missed their golden opportunity following a shock 4-2 defeat to relegation contenders Magesi.
Sunday’s NFD results:
Thanda Royal Zulu 2-0 Santos
Magesi 4-2 Royal Eagles