Suspensions afforded Masandawana the chance to give Kennedy Mweene, Bangaly Soumahoro, Wayne Arendse, Tiyani Mabunda, Sphelele Mkhulise and Jose Ali Meza a run out.
Soumahoro should've given the Brazilians the lead inside the 14th minute, but his header from a free-kick proved too comfortable to handle for Obakeng Naane.
VUT went forward and brought Mweene to some work with a free-kick from the edge of the six-yard area by Reitumetse Hlongwane three minutes before the half-hour mark.
Lebohang Maboe quickly shifted momentum back to the Brazilians a minute later and forced Naane into a near post save with a decent strike from point-blank range.
Mkhulise was next to go in search of the opener after combining with Keletso Makgalwa, but Naane once again denied the Brazilians with a smart save following the half-hour mark.
Sundowns went ahead nine minutes after the halftime break when Arendse met Meza's corner to head into the top corner amidst defensive pressure.
The lower-tier side immediately got a lifeline after a foul from Nicholus Lukhubeni inside the area led to a penalty, but Hlongwane skied over the top of Mweene's goal.
Phakamani Mahlambi replaced Meza following the 69th minute after the Brazilians introduced their first substitution of the match.
Mahlambi's arrival proved timeous as he combined with a supply from Maboe to give his side their second with an easy tap-in three minutes later.
VUT still pushed for a comeback despite trailing by two goals, however Masandawana locked up the contest to confirm their quarter-final passage.
Sundowns: Mweene, Lukhubeni, Lakay, Soumahoro, Seabi, Arendse, Mabunda, Makgalwa, Mkhulise, Maboe, Meza.
Subs: Pieterse, Madisha, Jali, Ngoma, Zwane, Mahlambi, Langerman.
VUT: Naane, Mokondo, Tema, Lekalakala, Sibisi, Mawelewele, Mampa, Bodiba, Chesane, Hlongwane, Mgidi.
Subs: Makhalanyane, Masango, Nkoe, Khoza, Raseasala, Nkosinathi, Mdlalose.