Haashim Domingo replaced Sameehg Doutie as the home side's sole change, with the newly-crowned Telkom Knockout champions also making one change as Lyle Lakay replaced the suspended Tebogo Langerman.
The Clever Boys asked the first question on two minutes with Thulani Hlatshwayo's half-volley from the six-yard area requiring Denis Onyango to palm for a corner kick.
Sundowns then went ahead when Andile Jali dispossessed Thabang Monare to play a cross to the back-post for Themba Zwane, whose scuffed effort set up Gaston Sirino for an easy tap-in after 15 minutes.
Domingo should restored parity moments later, with a smart attempt forcing Onyango to a save followed by a first-time volley from the near side flashing wide.
Wits waited until the final minute of the half to level matters after Gift Motupa met a cross from Deon Hotto to head beyond Onyango.
Thapelo Morena looked to restore Masandawana's advantage five minutes after the halftime break, but Wits goalkeeper Ricardo Goss parried the wing-back's effort from point-blank range.
Wits provided more danger signs a little later, but Masandawana had the more clear openings as Motjeka Madisha headed against the upright after 64 minutes following Sirino's corner.
Sundowns threw on their first change ten minutes to full-time, as Keletso Makgalwa, who scored his first league goal last week against Stellenbosch FC, came on for Zwane as the visitors looked for a later winner.
However, neither side could come up with the goods in the latter stages as Masandawana moved up to second spot while Wits find themselves in fourth position.
Wits: Goss, Macheke, Hlanti, Mkhwanazi, Hlatshwayo, Alexander, Domingo, Monare, Motupa, Pelembe, Hotto.
Subs: Petersen, Douhadji, Nange, Doutie, Khunyedi, Macuphu, Dzvukamanja.
Sundowns: Onyango, Morena, Lakay, Lebusa, Madisha, Kekana, Zwane, Jali, Affonso, Mkhulise, Sirino.
Subs: Mweene, Arendse, Maboe, Ngcongca, Makgalwa, Mabunda, Vilakazi.