Mauricio Affonso, who missed the 1-0 win over Polokwane City in their last Absa Premiership clash of the year returned, with Sphelele Mkhulise dropping to the bench while Mosa Lebusa failed a late fitness test.
The Brazilians' last trip to Algeria ended with a 2-0 win over Entente Setif in the 2016 group stages, with the latter later disqualified from the competition altogether.
A rather frantic start to the match put the Tshwane giants on the back foot, with Sundowns goalkeeper Denis Onyango called into action to grab hold of a decent shot from Zakaria Benchaa on 13 minutes.
Masandawana began enjoying more openings closer to halftime, as Gaston Sirino came close to profit from Affonso's ball with the visitors looking for a second group stage win.
A chance seconds from the break put Hlompho Kekana in with a shot from the edge of the area, but the skipper watched his attempt deflected to safety.
The first-ever goal in this fixture arrived on 58 minutes when Kekana made good use of a defensive error to skip past the Alger shot-stopper and fired into an un-guarded net.
Surprisingly minutes after netting the opener; Kekana was removed as Pitso Mosimane threw in Tiyani Mabunda across the middle of the park.
Alger upped the tempo in desperate pursuit of the equaliser and as the match dawned, Onyango was called to stave off a powerful strike from Aymen Mahious in the final 15 minutes.
Masandawana sustained the onslaught and collected three points to maintain top spot in Group C.
USM Alger: Zemmamouche, Meftah, Kheiraoui, Hamra, Cherifi, Koudri, Benkhelifa, Zouari, Benhamouda, Ardji, Benchaa.
Sundowns: Onyango, Ngcongca, Langerman, Madisha, Arendse, Jali, Kekana, Zwane, Morena, Sirino, Affonso.
Subs: Mweene, Soumahoro, Mabunda, Lakay, Vilakazi, Maboe, Mkhulise.