The Brazilians made three changes from the win over Jwaneng Galaxy in the CAF Champions League, as Denis Onyango, Rivaldo Coetzee and Themba Zwane returned to the line up.
Sundowns didn't waste time to signal their intent in the opening minutes, as a first-time shot from Peter Shalulile in the centre of the area forced an outstretched hand from Oscarine Masuluke.
Masuluke was put to work again towards the 20th minute after he pushed across his area to palm a curling free-kick from Zwane for a corner-kick.
Baroka remained on the ropes a few minutes before the half-hour mark with a ball from the left-side meeting Shalulile, who headed against the top of the woodwork.
Bakgaga Ba Ga Mphahlele continued to live dangerously in additional time after a towering header from Shalulile following a ball from the left hit the underside of the crossbar.
Masuluke carried his first-half display into the second stanza when he made an acrobatic save to steer Mothobi Mvala's header from a corner over the top.
However, the lanky shot-stopper was finally beaten as a curling low free-kick from Lyle Lakay on the cusp of the area nestled into the bottom-corner of the net on 56 minutes.
Gaston Sirino, who was embroiled in a transfer battle recently, made his first start of the season for Masandawana four minutes later after coming off the bench for Aubrey Modiba.
The hosts finished with ten players after Denwin Farmer upended Shalulile outside the area three minutes from time, while Masuluke palmed George Maluleka's strike over later on.
Zwane put Bakgaga out of their misery when he collected a low ball in the area from Sirino to curl into the top corner to send Sundowns three points clear of second-place Swallows.
Baroka: Masuluke, Mphahlele, Gebhardt, Shozi, Farmer, Kambala, Patjie, Mosele, Monama, Mgaga, Phiri Jr.
Subs: Chipezeze, Kgoetyane, Jampies, Mahlonoko, Nkhona, Mogale, Makume, Bowali, Mathiba.
Sundowns: D.Onyango, Morena, Lakay, Nascimento, B.Onyango, Coetzee, Mvala, Maboe, Zwane, Modiba, Shalulile.
Subs: Mweene, Jali, Sirino, Kapinga, Maluleka, Mdhluli, Langerman, Makgalwa.