Denis Onyango made a welcome return to Masandawana's goal, while Mauricio Affonso started for the first time, as Chippa handed a first start to striker Augustine Kwem.
Chippa drew first blood 12 minutes in, as Kwem introduced himself to the South African scene with a neat finish after slicing through the defence from Tercious Malepe.
The Chilli Boys immediately threatened a second shortly thereafter, with Masandawana disjointed in defence though Elvis Moyo specifically couldn't capitalise.
Chippa opened the far side ten minutes to halftime when Lehlogonolo Masalesa played a one-two with Kwem to go one-on-one with Onyango, who produced a fine save to keep the scoreline at one.
Affonso beat Patrick Tignyemb to a high cross from Tebogo Langerman two minutes before the break, but the Uruguayan failed to head home whilst Gaston Sirino flashed the upright a minute later.
Sundowns went for pace in attack a minute after halftime, as Phakamani Mahlambi came on for Jose Ali Meza. Mahlambi made an instant impact when his pace into the area proved too much for Kelvin Moyo, who conceded a penalty which Sirino fired home on 58 minutes.
Eight minutes later, Chippa reclaimed the advantage when Silas Mayiza's side-footer from the left looped over Onyango to nestle the far corner of the net following a free-kick.
Sundowns probed, probed and levelled in the final 20 minutes when Sirino made the most of poor handling from Tignyemb to complete his brace by finising into an empty net.
No goals arrived afterwards as the contest went to extra-time, which had Chippa's Malepe dismissed ten minutes in after disputing a refereeing decision.
After there were no goals in extra-time, the Brazilians bagged the honours via the penalty shoot-out, with Thapelo Morena netting the winning kick whilst Masalesa missed the final kick.
Chippa: Tignyemb, Damons, Modisane, K.Moyo, E. Moyo, Mahola, Maselesa, Maziya, Twala, Malepe, Kwem
Subs: Mothwa, R Manzini, L Manzini, Reid, Lentjies, Maphangule, Maphanga
Sundowns: Onyango, Morena, Madisha, Lebusa, Langerman, Mabunda, Kekana, Vilakazi, Sirino, Meza, Affonso
Subs: Pieterse, Ngcongca, Jali, Mahlambi, Lakay, Coetzee, Mkhulise