A stunning 88th-minute goal by Zeliat Nkhoma secured the win, giving Malawi a vital edge heading into the second leg in Tshwane on May 11.
The match was a tactical battle, with Malawi's late strike breaking South Africa's resolve in front of a passionate home crowd.
The game started cautiously, with both teams prioritizing defensive structure. Malawi, coached by Kalisto Pasuwa, adopted a compact 4-4-2 to neutralize South Africa's possession-based play, led by coach Molefi Ntseki.
Bafana controlled 54% of possession but struggled to penetrate Malawi's backline. Malawi's Wongani Lungu tested South Africa's goalkeeper Mondli Mpoto with a 20-yard shot in the 22nd minute, while Bafana's Tebogo Potsane fired narrowly wide from a corner in the 35th minute.
The teams went into the break level, setting up a crucial second half.
The second half saw Malawi grow bolder, exploiting the flanks to stretch South Africa's defence. Ntseki's substitutions aimed to secure an away goal, a priority he emphasized pre-match, but Malawi's tactical discipline frustrated Bafana.
The turning point came in the 88th minute when Zeliat Nkhoma, a rising star for the Flames, latched onto a precise through-ball and rifled a low shot past Mpoto to make it 1-0.
South Africa pressed desperately in stoppage time, but Malawi's defence, led by their resolute center-backs, held firm. The final whistle confirmed Malwai's win.
Malawi will come to South Africa in an advantageous position as a draw away would be enough for them to go through.
The second leg will be played at Loftus Stadium on Sunday, May 11.