Sphelele Mkhulise missed out through injury but Gaston Sirino made a return, while Mosa Lebusa and Anele Ngcongca came as one of Sundowns' three changes from the draw with Bidvest Wits.
Sundowns were on the attack in the opening ten minutes after a long ball from Denis Onyango found Sirino, who teed-up Themba Zwane for a shot but his effort was thwarted.
After constant probing, Masandawana went ahead ten minutes to halftime after Thapelo Morena connected with a ball out wide to head into an empty net.
Aymen Mahious clawed the visitors level with their first real attack in the final minute of the half as he headed home from poor defending.
However, Sundowns restored their advantage seconds from the restart after Sibusiso Vilakazi finished off a flowing move.
Alger pushed for the equaliser after both sides eased into the match following a frantic first half, but Tebogo Langerman accompanied by Onyango put his body on the line to stop the danger.
Sundowns looked for a second win over the Algerians to progress to the quarterfinals, having won the reverse fixture 1-0 towards the end of last year.
Masandawana introduced their first substitution under the final ten minutes, as Lebohang Maboe filled in for Sirino.
The Algerians got the chance to draw level on 86 minutes when Vilakazi conceded a penalty in the area. However, Mohamed Meftah fired against the crossbar, as Sundowns claimed victory and a spot in the last eight.
Sundowns: Onyango, Ngcongca, Langerman, Madisha, Lebusa, Jali, Kekana, Zwane, Morena, Sirino, Vilakazi.
Subs: Pieterse, Arendse, Mabunda, Lakay, Nascimento, Makgalwa, Maboe.
USM: Zemmamouche, Meftah, Oukkal, Hamra, Cherifi, Belarbi, Benkhelifa, Mahious, Benhamouda, Ardji, Benchaa.