Zimbabwean hitman Evans Rusike bagged the winner at Lucas Moripe Stadium to set up a semi-final date with SuperSport United, while champions Bidvest Wits will meet Cape Town City in the other last-four tie.
Sundowns coach Pitso Mosimane notably brought on new signings Manyisa and Lebese late into the contest, but the former Soweto-based stars were unable to help the kings of Africa find a way back.
Maritzburg counterpart Fadlu Davids likewise handed out debuts, introducing marquee recruit Siyanda Xulu and ex-Baroka attacker Mxolisi Kunene off the bench in Atteridgeville.
Khama Billat had an early opportunity for the hosts but directed a tame shot straight at goalkeeper Bongani Mpandle after being released by Hlompho Kekana's ball over the top.
At the other end, Zambian net-minder Kennedy Mweene, who was handed a rare start ahead of sick teammate Denis Onyango, was alert to gather a low effort from Lebohang Maboe.
Maritzburg threatened again when Pogiso Sanoka misdirected a free header in the box off a corner from Deolin Mekoa.
Sheldon van Wyk tried his best to draw first blood on the half-hour mark for the visitors, but was unable to make proper contact with Rusike's cross from the right at full stretch.
Denis Weidlich also came close as he shot wide in the box under pressure from the backtracking Sibusiso Vilakazi after combining smartly with Van Wyk down the left flank.
Tebogo Langerman tried his luck from range soon after but Mpandle comfortably gathered.
Both teams had great chances on the stroke of half-time, as Maboe's curling attempt was brilliantly foiled by a diving Mweene, while Billiat should have hit the target from inside the area for the Tshwane giants.
Sundowns started the second stanza strongly, as Thabo Nthethe's header hit the post in the 52nd minute.
However, Rusike pounced from close range six minutes later to give United the lead.
The diminutive Billiat nearly equalised in the 67th minute but glanced a header narrowly off target following a cross from the right by Thapelo Morena.
The Brazilians pressed forward in the closing stages, with Kekana coming repeatedly close to equalising at the death, but Davids' side held their nerve to come away victorious.