This came after their 3-1 win over Jwaneng Galaxy in their first round second leg match at Loftus Versfeld Stadium on Tuesday evening.
Kermit Erasmus opened the scoring before Mothobi Mvala and Thapelo Morena extended Masandawana’s lead.
Meanwhile, Tebogo Sembowa grabbed Botswana champions Galaxy’s late consolation goal.
Masandawana were looking to avoid a defeat in order to advance to the group stage, having claimed a 2-0 win in the first leg in Lobatse a fortnight ago.
Kennedy Mweene, Aubrey Modiba, and Kermit Erasmus made their way into the starting eleven from the one that did duty in Lebatse Stadium.
On the other hand, Galaxy were hoping to cause an upset by eliminating a much-fancied Sundowns side, who looked set to reach the Champions League group stage for the sixth year running.
Mngqithi’s counterpart Losikalame Keatlholetswe made three changes to the team which took on Masandawana in Botswana.
Thabang Sesinyi, Gofaone Molapi and Gilbert Baruti were recalled to the starting line-up.
Galaxy threatened first through former Orlando Pirates midfielder Ricardo Lourenco.
However, his deflected shot was well saved by Mweene in the Sundowns goalposts a few minutes into the game.
Sundowns will be in action this weekend as they take on Baroka FC in a Premier Soccer League match at the Peter Mokaba Stadium on Saturday.