Surprise Moriri and Lebohang Mokoena got a goal in either half at Charles Mopeli Stadium, handing Ea Lla Koto their first home defeat in the Premiership this season.
The Brazilians take a three-point lead at the top of the log, where they will stay for two months.
In the eighth minute Sundowns took the lead when Moriri slammed in a close-range shot, after a free-kick from the in-form Teko Modise fell to him inside the 18-yard area.
Modise had a powerful shot on target soon after, but Kennedy Mweene was up to the task and tipped it around the post.
Stars then had a couple of chances to draw level, but Sadate Ouro Akoriko shot wide before Saname Wome blasted over the bar.
Then, 10 minutes before half-time, Clayton Daniel and then Wome both shot wide, in what could have been game-changing chances.
Moriri almost bagged a brace before the break, against from a Modise free-kick, but his header from close range was grabbed by Mweene.
The second half began with Sundowns coming out all guns blazing, and Stars playing on the counter-attack, and both sides missed a number of chances.
Edward Mnqele forced a save out of Wayne Sandilands on 54 minutes, but on the hour mark Sundowns extended their lead, when Mokoena connected with Modise's cross to make it 2-0.
Mnqele then blasted over the bar 13 minutes from time.
Free State Stars were reduced to 10 men in the final minutes, when Akoriko was sent off, although they had a chance to get one back when substitute Morou Zakari fired a header over in injury time.