An own-goal from Pere Ariweriyai and one each from Nyasha Mushekwi and Lebohang Mokoena handed Sundowns the points, while Eleazar Rodgers kept his name in the top-scorer's race with a consolation goal for Santos.
Sundowns controlled the match from the first whistle, but battle to create any scoring opportunities, losing possession in the final third with some careless passing.
In fact, their first goal came from a Santos player, when a hapless Ariweriyai headed powerfully into his own net after a speedy cross by Elias Pelembe.
Sundowns continued to struggle to make their dominance count as the game dulled down. Finally, seven minutes from half-time, Lebohang Mokoena sent a pinpoint cross through, picking out an unmarked Nyasha Mushekwi, who made no mistake with a clinical header from six yards – his ninth League goal of the season.
Santos tried to fight their way back into the match in the second half, but Sundowns kept hold of the ball. Some sloppy defending in the 63rd minute gifted Hlompho Kekana a shot, and he fired a low drive into the bottom right-hand corner to make it 3-0.
The Brazilians sat back after going three up, and Rodgers got one back, with a fine finish from 10 metres out – his 11th of the season.
But it was far too little too late, and Santos remain second from bottom, while Sundowns go top on goal-difference.