Sundowns made four changes, as they handed Divine Lunga his debut against his former side, while goalkeeper Reyaad Pieterse and Pavol Safranko got their first starts of the season along with a re-call for Haashim Domingo.
The Brazilians enjoyed a dream start after Peter Shalulile opened the scoring in fourth minute with a tap-in at the second time of asking after shot-stopper Sifiso Mlungwana spilled a strike from Thabiso Kutumela.
Velemseni Ndwandwe almost levelled matters for Arrows two minutes later with a snap shot from just outside the box that produced a great out-stretching save from Pieterse towards the bottom corner.
The hosts kept Abafana Bes'thende pinned back in their own half and Lunga eventually made it 2-0 just before half-hour mark with a glancing header from Kutumela's cross.
Sundowns continued to threaten going forward in the closing phase of the first stanza, but Kutumela was unlucky not add a third goal on the stroke of half-time with a low diving header that came off the far post.
Masandawana rested Themba Zwane at half-time, as he was replaced by Gaston Sirino while Lehlohonolo Seema made a double change with Sbonelo Cele and Simo Mbhele replaced Pule Mmodi and Ndwandwe.
The Brazilians were in control of the contest, although they were not rushing to reach the final third as Arrows struggled to gather any momentum.
Masandawana were forced into a change in the last five minutes after Pieterse was stretchered off the pitch following his collision with Nkosinathi Sibisi and he was replaced by fellow goalkeeper Ricardo Goss.
Maema got the third goal for the hosts deep in stoppage time with a sensational curler into the top corner as Sundowns reached the final with a 4-1 aggregate win and will meet the winner between Swallows and Cape Town, in the other semi-final second-leg, in the final.
Sundowns: Pieterse, Lunga, Lakay, De Reuck, G. Kekana, Jali, Zwane, Domingo, Kutumela, Safranko, Shalulile
Subs: Goss, Maluleka, Modiba, B. Onyango, Mkhulise, Sirino, Maema, Erasmus, Vilakazi
Arrows: Mlungwana, Sibisi, Zuke, Mantshiyane, M.Dube, Dlamini, Ndwandwe, Mmodi, Sibiya, Mutizwa, Gumede
Subs: Mbaeva, Mathiane, Ndlovu, Magawana, Khumalo, Magubane, Cele, Nkosi, Mbhele