Sundowns made just one change to their side, with Lebohang Maboe coming into the attack alongside Themba Zwane and Gaston Sirino.
The Brazilians had two chances in quick succession in the opening four minutes. First, Mothobi Mvala had his shot blocked by the defender before Lyle Lakay had a shot that narrowly missed the upright.
Soon after, Sundowns keeper Denis Onyango smartly saved Ananias Gebhardt's header from a Gerald Phiri Jr free-kick as the visitors began to up the tempo.
With chances in open play few and far between, Lakay's low free-kick deflected off the wall before being saved by Bakgaga shot-stopper Elvis Chipezeze in goal.
Shortly after the half-hour mark, Mkhulise floated a delivery to the far post where Gaston Sirino met it first time only to see his effort go over the bar.
Phiri delivered the free-kick into the box and Manuel Kambala took a right-footed shot on the right side of the six yard box but missed to the right Soon after, Masiya got to the byline on the left-hand side after a lovely little flick around the corner and he cut the ball back for Joslin Kamatuka but Mosa Lebusa made a timely interception.
Kermit Erasmus, who had been brought on as a replacement for Mvala, made the desired impact with a perfect through-ball for Gaston Sirino and the Uruguayan curled the finish towards the far post with Chipezeze almost keeping it out but his hand to the ball was not strong enough.
And it was 2-0 just a couple of minutes afterwards. Mkhulise played a clever little ball for Erasmus inside the box whose left-footed strike was parried into the path of Shalulile, who had an easy tap-in.
Baroka had been utterly dominated by Sundowns in the second half and were saved by the woodwork when Erasmus delivered to the back post and Lakay's side-footed half-volley hit the left-hand upright.
Baroka substitute Mfanafuthi Shozi then had an effort cleared off the line by Ricardo Nascimento. But in the end, Thoka Matsimela's side could not prevent the Brazilians from keeping their excellent defensive record intact with yet another clean sheet.
Sundowns: Onyango, Lakay, Lebusa, Nascimento, Mvala, Coetzee, Sirino, Mkhulise, Zwane, Maboe, Shalulile
Subs: Goss, Modiba, Morena, Kapinga, De Reuck, Domingo, Jali, Erasmus, Mkhuma
Baroka: Chipezeze; Mphahlele, Makume, Gebhardt, Jampies; Mosele, Kambala; Masiya, Phiri, Mgaga; Makgopa
Subs: Masuluke, Seema, Shozi, Kgoetyane, Ntemane, Patjie, Kamatuka, Mogale, Monama