After an end to end first half, Golden Arrows went into the break with a 1-0 lead courtesy of Boy Gumede’s 13th minute strike.
The hosts thought they had done enough to progress to the next round, but veteran striker Lehlohonolo Majoro struck in added time to ensure that the game goes to extra time.
After receiving a second yellow card because of a reckless tackle, Ntsako Makhubela was given his marching orders right at the end of extra time.
Zimbabwean international Danny Phiri missed a penalty for Arrows while Luvuyo Memela made no mistake and scored the fifth penalty to make it 5-4 for the visitors who progressed to the next round.
Elsewhere, Cape Town City progressed to the last 16 of the competition after a resounding 4-0 victory against Bloemfontein Celtic.
Tashreeq Moris took home the match ball after scoring a hat-trick. Thabo Nodada was also on target for City.
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By Prince Sobayeni