The game was off to a slow start and the first real shot in anger arrived for Masandawana around the middle of the first stanza with Haashim Domingo shaving the post.
Just before the break the breakthrough arrived when Terrence Mashego cut the ball across the Cameroon outfit's goal, where Sylvestre Materne accidentally found the back of his own net with a failed clearance.
Les Cotonniers came close to equalising towards the latter stages of the game as Mekong hit the outside of the Sundowns post.
The result was secured by Abubeker Nasir in the 86th minute as he made it 2-0, before a consolation strike for the visitors via Moshood Kasali.
The win put Sundowns top of Group B with a four-point gap over second-placed Al Ahly, while Coton Sport are rock-bottom having lost six from six.
Meanwhile, the Brazilians had even more cause for celebration as they secured the DStv Premiership title thanks to a draw between SuperSport United and Chippa United.