Captain Hlompho Kekana, Tebogo Langerman, Gaston Sirino, Mauricio Affonso and Thapelo Morena were welcome returnees for Sundowns, while Richard Ofori returned from suspension to take over from Mpandle between the sticks for Maritzburg.
A collision involving Onyango and Mosa Lebusa two minutes from kick off nearly culminated in the opener, but Daylon Claasen dragged an inviting chance with a gaping goal wide of target.
Sundowns, who haven't won a cup encounter against the Team of Choice since a 2-0 win in the 2011/12, struggled to carve out any big openings in the first half, despite enjoying more of the ball in the latter stages of the half.
Judas Moseamedi, who single-handedly tormented Kaizer Chiefs in the last round, lobbed into an empty net five minutes to halftime after a miscommunication between Onyango and Mosa Lebusa to give Maritzburg the lead.
Ten minutes into the second half, Masandawana drew level after poor positioning from Ofori allowed to nod home after Ofori was unable to clear Sirino's cross.
Maritzburg coach Eric Tinkler introduced a change in order to regain the lead, as Daylon Claasen made room for attacker Deolin Mekoa on 68 minutes.
The Team of Choice weren't able to spring a comeback, as Affonso rose well to head home from a corner by Sirino to complete his brace and put Sundowns ahead with 16 minutes remaining.
United looked to have sent the match to extra-time when Moseamedi headed in at the near post, but the effort was ruled out for offside as Masandwana went on to claim the crown.
Maritzburg: Ofori, Morgan, Kunene, Mngonyama, De Reuck, Allie, Buchanan, Claasen, Shandu, Timm, Moseamedi.
Subs: Mpandle, Sanoka, Jappie, Mekoa, Lea'alafa, Kutumela, Augusto.
Sundowns: Onyango, Langerman, Morena, Madisha, Jali, Kekana, Lebusa, Zwane, Mkhulise, Sirino, Affonso.
Subs: Mweene, Arendse, Lakay, Ngcongca, Makgalwa, Mabunda, Vilakazi.