Teboho Mokoena and Peter Shalulile found the back of the net for the defending champions while Thabiso Lebitso scored a consolation goal late on for the Chilli Boys.
Masandawana took the lead in the 14th minute when Mokoena connected with a header after an excellent cross from Aubrey Modiba.
The visitors almost hit back immediately but Etiosa Ighadaro saw his goal-bound effort parried away by Sundowns goalkeeper Ronwen Williams.
The hosts though continued to dominate proceedings in terms of possession in first half but failed to create further openings in the Chippa defence.
Namibian forward Shalulile entered the fray as an early substitute after interval and the move paid immediate dividends.
Fellow sub Sifiso Ngobeni put a cross into the box and Shalulile got his head to the ball for his seventh goal of the season.
Chippa provided a surge late in the game as they tried to get one back and their efforts were rewarded in stoppage time when Lebitso guided a header past Williams from Ronald Maarman's cross.
The Chilli Boys then poured forward in search of the equaliser but Sundowns held them at bay to extend their winning run to 10 league matches and go 13 points clear at the top of the table.