The Brazilians were keen to return to winning ways in the league having drawn their last two matches against Polokwane City and Bidvest Wits.
Speedy forward Phakamani Mahlambi, who scored during the 1-1 draw against Wits last weekend, was replaced by experienced winger Anthony Laffor.
The Citizens were targeting their second successive victory in the league having edged out Maritzburg United 3-2 in a thrilling encounter last weekend.
Promising winger Gift Links, who inspired City to victory over Maritzburg by grabbing a goal and an assist, unsurprisingly kept his place in the starting line-up.
The hosts were the better side in the opening exchanges with Laffor, Lebohang Maboe and Gaston Sirino all looking lively for the Brazilians.
Sirino had a good opportunity to put Sundowns into the lead following some great work by Laffor, but the former's effort was brilliantly saved by Peter Leeuwenburgh in the City goal.
However, the tall Dutch goalkeeper was beaten in the 22nd minute when Tebogo Langerman's excellent long pass sent Maboe through on goal and he scored to make it 1-0 to Sundowns.
It did not come as a surprise as the defending league champions came into the match having netted 25% of their goals between the 15th minute and 30th minute in their league games this season.
Sundowns continued to dominate after taking the lead and Leeuwenburgh had to produce two great saves to deny Tebogo Langerman and Maboe.
The saves ensured that the first half ended with Sundowns deservedly leading 1-0 at the interval.
The Citizens came back rejuvenated following their half-time team talk with Benni McCarthy and they were awarded a penalty after Langerman was adjudged to have handled the ball in the Sundowns box.
Riyaad Norodien then stepped up and beat Sundowns shot-stopper Kennedy Mweene from the spot to make it 1-1 in the 47th minute with the winger netting his second goal in as many games.
However, parity was only restored for 13 minutes as the hosts piled pressure on the visitors and Laffor made it 2-1 to Sundowns with a powerful first-time shot after Themba Zwane's effort was blocked.
McCarthy reacted by introducing experienced striker Kermit Erasmus as the Citizens looked to grab a late equalizing goal in the closing stages of the match.
Pitso Mosimane responded by introducing an offensive-minded player, Mahlambi as the Brazilians opted to continue to attack rather than sit back and defend their slender lead.
The move paid off as Mahlambi proved to be an inspired substitution as he scored with a tap in after being set-up by Zwane with three minutes left on the clock.
City did grab a late goal through Erasmus, who scored with a thunderous long-range shot in the 90th minute, but the goal proved to a mere consolation as Sundowns held on to win 3-2 on the night.
The victory took the Brazilians to the top of the league standings - a point above second-placed Bidvest Wits, while the Citizens remained fourth on the table.