There were also opening day victories for Botswana and Uganda as the competition got off to a thrilling start.
Banyana Banyana hit the front inside seven minutes as Khanya Xesi netted a fine opener after a lively start from both teams.
Nothando Vilakazi doubled the lead for the home side before the 20-minute mark and at that stage it looked as though they were cruising to victory.
But just two minutes later Madagascar were back in the contest as Sarah Rasoanandrasana pulled a goal back from the penalty spot, and a short while later they hit the post from a free-kick too.
The hosts were reduced to 10 players when Thato Letsoso received a second yellow card in the dying minutes, but Madagascar were not able to capitalize on their numerical advantage.
In the opening match of the tournament, Botswana cruised to a 2-0 victory over Malawi in their Group A clash.
The Mares netted early on as skipper Lesego Keleboge found the back of the net to settle their nerves.
Malawi certainly had their chances to equalize, but were not able to find the back of the net and when Lesego Radiakanyo added a second for Botswana 13 minutes from time, the points were safe.
In Group C, Uganda edged Eswatini in a seven-goal thriller after taking a 3-0 lead into the break.
Hasifah had the East African guest nation in front inside two minutes with a fine shot, before Resty Nanziri struck the crossbar as the Ugandans dominated the play.
It was 2-0 on the half-hour mark as Alupo Norah doubled the advantage with a well-taken goal and Nanziri added the third just before the break.
But Eswatini were much better after the break as a quick counter-attack saw Tenanile Mgcamphalala reduce the deficit.
That became just a single goal with 13 minutes remaining when Celiwe Nkambule latched onto a long ball and finished.
But Uganda sealed the points four minutes later as Nassuna grabbed her second, though there was still time for a nervy finish as Cebile Shongwe produced a brilliant lob to pull Eswatini back to just a single goal behind.
The action continues on Thursday (13 September) when 2017 runners-up Zimbabwe host Namibia in their Group C opener.
Zimbabwe will want to regain the title they won in 2011, but come up against a difficult opponent in the Namibians. That match kicks-off at 10h00.
Focus will then switch to Group B as Central African guest nation Cameroon debut in the competition with a fixture against Mozambique.
Cameroon are the highest ranked team in the tournament at number three on the African continent and like South Africa and Zambia, are preparing for the African Women’s Championship finals in Ghana starting in mid-November.
Their match with the Mambas gets under way at 13h00.
The final game of the day will see Zambia tackle Lesotho in another Group B fixture at 15h30.
All the games will be played at the Wolfson Stadium and entrance for fans is FREE.
All Wolfson Stadium
Botswana 2 (Lesego Keleboge, Lesego Radiakanyo) Malawi 0
Eswatini 3 (Tenanile Mgcamphalala, Celiwe Nkambule, Cebile Shongwe) Uganda 4 (Hasifah Nassuna 2, Alupo Norah, Resty Nanziri)
South Africa 2 (Khanya Xesi, Nothando Vilakazi) Madagascar 1 (Sarah Rasoanandrasana)
All Wolfson Stadium
10h00 (08h00 GMT) – Zimbabwe vs Namibia
13h00 (11h00 GMT) – Cameroon vs Mozambique
15h30 (13h30 GMT) – Zambia vs Lesotho
GROUP A P W D L GF GA PTS
Botswana 1 1 0 0 2 0 3
South Africa 1 1 0 0 2 1 3
Madagascar 1 0 0 1 1 2 0
Malawi 1 0 0 1 0 2 0
GROUP B P W D L GF GA PTS
Cameroon 0 0 0 0 0 0 0
Lesotho 0 0 0 0 0 0 0
Mozambique 0 0 0 0 0 0 0
Zambia 0 0 0 0 0 0 0
GROUP C P W D L GF GA PTS
Uganda 1 1 0 0 4 3 3
Namibia 0 0 0 0 0 0 0
Zimbabwe 0 0 0 0 0 0 0
Eswatini 1 0 0 1 3 4 0
Matches Played: 3
Goals scored: 12
Biggest victory: Botswana 2 Malawi 0 (Group A, September 12)
Most goals in a game: 7 – Eswatini 3 Uganda 4 (Group C, September 13)
2 goals – Hasifah Nassuna (Uganda)
1 – Lesego Keleboge (Botswana), Tenanile Mgcamphalala (Eswatini), Resty Nanziri (Uganda), Celiwe Nkambule (Eswatini), Alupo Norah (Uganda), Lesego Radiakanyo (Botswana), Sarah Rasoanandrasana (Madagascar), Cebile Shongwe (Eswatini), Nothando Vilakazi (South Africa),Khanya Xesi (South Africa).