Denis Onyango's absence brought Kennedy Mweene in goal for Sundowns as Anele Ngcongca returned in defence, while Lebohang Maboe started in place of the injured Jose Ali Meza.
Highlands made a flying start as early as the fourth minute when Mothobi Mvala cracked the post with a shot from outside the danger following good work.
Sundowns dusted off the slow start and got in to stride in the next couple of minutes, but the reigning champions couldn't breach the Lions of the North defence despite their attacking quality.
The home side maintained pressure on 25 minutes as a decent strike from Themba Zwane required Thela Ngobeni getting to work to pull off a smart save. However, Sundowns missed a big chance five minutes to the break when Gaston Sirino broke away from a challenge to curl wide of the intended target.
Masandawana were quick out of the starting blocks a minute from halftime as Thapelo Morena flashed wide metres from the initial target. Ngobeni pulled off another fine block 12 minutes from the break, smothering the efforts of Sirino who launched a smart attempt after barging through the attacking area.
Sundowns made the evening's first substitution 64 minutes in with Mauricio Affonso replacing Maboe in the final third of the pitch. The move nearly paid off as Affonso set up Morena for a close range finish, but the Bafana Bafana international fired against the woodwork.
Affonso made his presence felt right at the death when one-touch passing involving Zwane and Sirino instigated the former to fire past Ngobeni for his third goal for the club.
As a result, the Brazilians go second on the table with the victory, two points behind league leaders Kaizer Chiefs ahead of Sunday's encounter.
Sundowns: Mweene, Langerman, Ngcongca, Madisha, Jali, Kekana, Lebusa, Sirino, Maboe, Zwane, Morena
Subs: Ngcobo, Vilakazi, Coetzee, Lakay, Mkhulise, Mahlambi, Affonso.
Highlands: Ngobeni, Mokoena, Mbhele, Msimango, Rae, Mbunjana, Williams, Mbatha, Shalulile, Mvala, Mogaila.
Subs: Peters, Fransman, Letsholonyane, Banda, Jooste, Motlafi, Ndoro.