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.
A Dithloriso Mphyane brace, combined with a Thembisani Nevhulamba strike and Karabo Litabe's own goal gave Magesi just their fourth win of the season, despite Jabulani Nene’s early goal and Sedwyn George’s 19th strike of the campaign.
Sunday’s NFD results:
Thanda Royal Zulu 2-0 Santos
Magesi 4-2 Royal Eagles