A goal six minutes from time by captain Hlompho Kekana settled the match after he had earlier incorrectly had another goal ruled out for offside.
The win moves Sundowns to seventh in the table, six points behind leaders BidVest Wits but with five games in hand. Baroka will spend the festive season break on the bottom of the table.
The first half was low on quality with Sundowns looking sluggish in possession and Baroka simply trying to contain them and hit back on the break.
Khama Billiat flashed a shot just wide with Sundowns' best chance of the half, while the home side should have taken the lead five minutes before the break.
Richard Matloga raced clear despite being four yards offside, rounded Sundowns keeper Wayne Sandilands, but could not steer his shot into an empty net from a tight angle. Ricardo Nascimento was able to clear the loose ball.
Baroka turned up the heat in the second half and had two excellent chances to score within in a few seconds. Matloga's header was well saved and Collins Makgaka put the rebound over the bar.
Billiat had an excellent chance at the other end when he found himself in a shooting position, but fired straight at Oscarine Masuluke in the home goal.
Kekana did get his goal six minutes from time when substitute Anthony Laffor produced a super cross and the captained crashed a bullet header past the helpless Masuluke.