Centre-back Keenan Abrahams scored the deciding penalty after Lyle Foster, who scored the equalizer with five minutes remaining on the clock before full-time, blasted Amajita’s third penalty take over the crossbar.
This winning result means that South Africa has won this Southern regional junior football tournament for the seventh time now.
It also sees Amajita coach Thabo Senong achieving a personal milestone by becoming the first South African coach to defend this title at Under-20 level.
In the first period of the match, Zimbabwe showed great tactical discipline at the back to thwart every attacking move South Africa created moving forward. Their approach worked as Amajita struggled massively to find breathing spaces to punish their opponents up in the final third.
In the second period, Zimbabwe scored an opener through their centre-forward Delic Murimba in the 64th minute. The striker simply looped the ball over Amajita goalkeeper, Khulekani Kubheka, who was way off his line to make the required save.
To help his side fight to come back in the game, Senong sacrificed two of his defenders in Malebogo Modise and Njabulo Blom for attacking players in Solly Khunyedi and Tashreeq Matthews.
That decision worked wonders as Amajita began to play with more verve in their attack to open up a stubborn Zimbabwean defence more pressing forward.
In the 85th minute, Foster scored his fifth goal of the tournament to keep Amajita in the game.
Foster walked away with this year’s COSAFA Under-20 Championship joint Top goalscorer, while Mkhuma finished as the Player of the Tournament.
In the 3rd/4th place play-off match, Angola subjected hosts Zambia to a 2-1 defeat to secure a third-place finish in the tournament.
Thabo Senong's side will now set sights on next year's Africa Cup of Nations tournament which will be held in Niger.
Amajita have been pitted in Group A alongside Niger, Nigeria and Burundi.
Group B consists of Ghana, Burkina Faso, Senegal and Mali.
The top four teams at the tournament will automatically qualify for the 2019 Fifa U20 World Cup in Poland.